The Phantom War
by SuperSonicSpeedFan
Summary: A hero fallen, an empire on the rise. A quest to change the past and save the future. An epic struggle between good and evil. Heroes must put aside their differences and come together to face off against a foe greater than ever before. — A more serious and detailed take on Sonic Forces, with much more character interaction and development, and without Classic Sonic or a major OC.
1. Prologue

**The Phantom War**

 _A Sonic Forces Rewrite_

* * *

Prologue

* * *

 _"Our world is ruined. By fire, and smoke. By acid and sulfur. By a man and his machines. By the empire and its legacy. But it wasn't always like this. Something happened, long ago, to change our world from a lush paradise into a polluted wasteland. It happened so long ago, and the empire destroyed so many historical records, we were never able to piece together what led to this dark reality we face."_

A gloved hand fiddled anxiously with a golden cuff as their owner listened to the words being spoken.

 _"But now... Now we do know. Chance, or perhaps fate, has delivered to us the knowledge and the opportunity to change our reality. That is why you have been brought before us."_

The summoned individual straightened imperceptibly, golden eyes staring attentively at the speaker as they continued their oration.

 _"The document we retrieved from the island tells of many important things. Not least of which is this: that a hero once stood against the rising evil, and beat it back again and again. He prevented the rise of the empire for many years. But one day, nearly 400 years ago now, he was defeated._ _With his defeat, and the lack of any being to stand in his place, the world quickly succumbed to despair and was subjugated by the first emperor._ _How or why he was defeated is not recorded._ _But the rough date is."_

The white-furred hedgehog breathed out as this new information sank in, his mental gears shifting as an idea presented itself, and suddenly he realized why they had called _him_ here for this.

 _"Silver the Hedgehog. Out of all the beings we have in our ranks, you alone have demonstrated the ability to harness the powers of a chaos emerald. Now that we have two of them with us, you should be able to create a time rift with them, and step back in time to before the world fell. Before the hero was defeated. Take the document with you, for it speaks of many things that will be of use to you. Thus armed with the knowledge of both future and past, prevent the hero's fall, and the Empire's rise. You have this one chance to change fate, and fix the world for us all. Never give up, because if you fail here, we are all lost."_

Two glowing gems were held in front of him, and he slowly reached out to take them, one in each hand. With a determined glint in his eyes, Silver nodded his head. "Then I will not fail." He vowed.

Tucking the emeralds into his quills for the moment, he turned his gaze to the document, quickly skimming over it. It painted a bleak picture of despair and guilt, and while a good portion of it was still a mystery, it revealed much that had been lost in the ages since it was written. The purpose of the island the document and emerald had been discovered on, the reason that island was trapped in a glacier, and the name of its sole former inhabitant. It also gave the name of the first emperor, the rough date of the hero's fall, and most importantly - the name of the hero himself.

 _Sonic the Hedgehog._ Silver turned the name over in his mind. _I will find you, and I will prevent this future from ever happening._

* * *

 **Author's Note: Hey there folks. This isn't the first story I've ever written, but it is the first that I've ever posted on this site. As such I'd appreciate any suggestions/reviews you have to offer. I don't know what my update schedule will look like for this, but I already have the first chapter pretty well flushed out, and it should be up within a few days.**

 **As for why I'm doing this, well...**

 **I like Sonic Forces. I think it's a fun game, despite being flawed in several ways. I honestly think the hate train has gone overboard. The game visually gorgeous, and it's not broken like 06 was. And the implementation of the custom character was done very well IMO.**

 **But there's no arguing, the plot and story was a disaster - full of holes, inconsistencies, and pointlessness. Classic Sonic had no purpose whatsoever. And the avatar story was a little to much "friendship is the magic solution to every problem". I like the avatar in the game, but I don't think it fits well with the story. So I'm not going to include the avatar/custom hero/OC in this story. In addition,** **I love the fact that Silver is back, but I'm upset they never had any real story for him. Same with Shadow. We finally get another game with Sonic, Shadow, and Silver all on the same side, and yet there's absolutely no depth to the story. So I decided to fix it. This is my idea of a Sonic Forces story that is actually captivating and interesting, without pointless classic Sonic or magic "friendship solves every problem".**

 **Questions, suggestions, and opinions are greatly welcomed and appreciated, so please don't hesitate to leave a review.**


	2. Breaking Dark

**Author's Note: I'm pleasantly surprised at how much attention and support this story has received in such a short time. Thank you all so much.**

 **To those who reviewed:**

 **bajy - Thank you, I'm glad you liked it. Here's the next chapter for you right now.**

 **IcyPinkFlower - Thank you! I'm happy to know my proofreading has kept typos out so far.**

 **Gadget The Critic - Sonic NextGen, this time with 100% less princesses.**

 **And without further ado...**

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Chapter 1 - Breaking Dark

* * *

Light was quietly fading over the southern hill country of Mobius. Sunset bathed the still and peaceful landscape in a golden glow, and the soft breath of a slow wind over the grassy slopes was the only natural sound to be heard. It was a beautiful scene, for anybody would have taken the time to enjoy it, but the only being in the area had no time for such simple pursuits. His dark form raced over the hills at supersonic speed, the sonic boom in his wake disturbing the otherwise peaceful atmosphere. Fast, focused, and determined, the figure had no care for anything other than his mission.

Perhaps once, in another lifetime, he would have enjoyed the scene. In his youth he would have appreciated the beauty of the natural world, and he would have delighted to share it with the one who had been like a sister to him. But that was long ago, before time and life had broken him and remade him into what he was now. He had left that self behind, and dwelling on the past was not something he cared to do again. With the sun slipping beneath the horizon behind him, Shadow the Hedgehog pressed onward into the darkness.

* * *

As the last vestiges of daylight faded away to the west, Shadow arrived at his destination. Slowing to a run, he climbed the final hill before crouching himself down atop a rocky bluff at the outskirts of a wide valley. Activating the communicator on his wrist, he spoke in a low tone: "Rouge. I've arrived at the coordinates."

A burst of static issued from the device before a sultry voice responded: "What can you see?"

From his vantage point, Shadow stared out at the valley below, from which rose a towering pyramidal structure, surrounded at its base by various industrial plants and power generators. "This is definitely one of the Doctor's facilities. A very large one at that. I suspect the shipments we traced here are part of something big."

His ally's frown at the deduction was detectable even without a face-to-face connection. "How big are we talking about here?"

"It's the biggest installation we've come across in years." Responded the ebony one as his eyes scanned the structure, illuminated by many various floodlights and searchlights. "Including the supporting structures and the security fencing, the base covers several square miles at least. It's amazing the Doctor managed to keep something this big a secret for so long." He shook his head. "Whatever he's doing here, it can't be good. I want to take a closer look myself before we send Omega in and start making noise."

"Do it to it Shadow" came the reply. "Just don't take too long. I know Omega is getting antsy."

"YOUR PATRONIZING TONE IS DETECTED AND NOT APPRECIATED." A robotic monotone broke in. "EVERY SECOND WASTED RISKS THE DOCTOR BECOMING ALERTED TO OUR PRESENCE. WE MUST STRIKE NOW."

"A few minutes won't hurt, Omega." Rouge fired back. "Besides, Shadow knows how to get in without being seen."

"EXCESSIVE DELAY WILL NOT BE TOLERATED."

"Just shut up and let me work!" Grumbled Shadow, as he switched off the communicator. _That robot is more trouble than he is worth sometimes._

Standing up and looking down into the compound below, Shadow reached into his quills to grasp the green chaos emerald, the only one currently in his possession. With a murmur of "chaos control", he vanished from sight.

* * *

Reappearing in a dark alley inside the compound near an entrance to the large pyramid, Shadow tucked the emerald away and darted inside. Ducking from corner to corner, avoiding robotic patrols and security cameras, he made his way into the heart of the structure. As he moved onward he passed through a multitude of factories and assembly lines, endlessly working to build the latest generation of eggpawns. Further in, the factories became much larger, machining and welding parts to what looked like giant death egg robots. _The Doctor is mass producing those now? How did he keep this a secret for so long, and how much time do we have before an army of those machines is let loose?_

With these troubling questions in mind, Shadow pressed further. A bad feeling was starting to manifest itself in his gut. Discreetly following a cart loaded with missile warheads, he found himself moving underground, into a large storage area carved out of the earth under the base. Nimbly climbing atop a storage rack, he surveyed the cavernous room in shock. Spread out for what seemed like miles were shelves and racks filled with warheads of every shape and size, missiles to mount them on, bombs of every type, thousands upon thousands of dormant eggpawns, and a plethora of other weapons and bots that had issued from the mind of the evil genius.

 _This is worse than I suspected. How long has he been stockpiling like this? And what else does he have hidden away like this facility was?_

As if in answer, a series of yellow lights started flashing through the room, and a robotic voice announced from loudspeakers that security was being heightened to yellow alert. Shadow immediately feared that he had been discovered, and he quickly made his way back up to the surface levels. But just as he reached the entrance to the pyramid and was preparing to chaos control back outside the compound, he looked up and realized why the base was on alert. Flying into a brightly lit and open hanger near the top of the pyramid, was a spherical open-topped vehicle.

 _The Doctor is here._

Quickly activating his communicator again, Shadow gave a brief update to Rouge. "This place is bigger than we could have imagined. Weapons and bots are being built and stockpiled here in massive numbers. Bigger mechs than we've seen in ages are being mass produced. And the Doctor himself is here."

"Sweet chaos." muttered Rouge. "How did we not know about this sooner? And Eggman is _there_?!"

"Yes. This place is far too large and heavily fortified for us to take down ourselves without a lot more preparation. I recommend we pull back and flush out a better strategy before we assault this place. Right now I'm going to trail the doctor, and see if I can find out exactly what he's planning. It can't be good."

"Alright. I'll tell Omega that we..." The bat suddenly went quiet. There was silence on the line for a moment, and Shadow was about to ask if she was still there, before she spoke up again in a low, worried tone. "I think we have a big problem Shadow."

"What is it?"

"As soon as he heard that the Doctor was on site, Omega turned off his comm and started his approach to the base. That stupid bucket of bolts is going to get himself killed!"

At that moment, as if to punctuate Rouge's statement, sirens started blaring all around and red lights flashed. A series of increasingly colorful expletives ran through Shadow's mind, and he groaned aloud.

"You would think a robot would have more sense than to charge into this armory guns blazing!" He yelled over the alarms as distant explosions sounded. "Hold on, I'm going to get him out of here!"

With a low whine, Shadow's hoverskates activated and he rocketed towards the source of the gunfire and explosions. Sentries spotted him, but they were destroyed before they could raise additional alarm. With a determined scowl Shadow quickly ripped through everything in his path, ruby eyes glinting in the electric light of the base they darted from target to target.

The voice of robot that had caused all this commotion suddenly sounded from communicator. "E-123 OMEGA REPORTING. EXTERMINATION PROCEEDING WITHOUT INCIDENT. DOCTOR EGGMAN SIGHTED. IN PURSUIT."

" _Extermination?!_ " Rouge practically screamed. "You idiot! You're going to get yourself killed! And Shadow too!"

"Hmph." Was Shadow's only reply. _Omega? Perhaps. Me?_ _Not likely._

"UNKNOWN ENEMY SIGHTED. ENGAGING."

Three more sentries went down as Shadow skated through the compound, as searchlights circled in vain trying to catch a glimpse of him. He quickly found and followed the trail of devastation left in Omega's wake, skating effortlessly above the flames and debris.

"POSITION COORDINATES LOST. SENSORS MALFUNCTIONING. DAMAGE TO PARIETAL LOBE REGION."

Shadow cursed under his breath and pushed himself to go faster, scaling the side of the pyramid on his way to the open hangar that the robot had pursued Eggman into, fighting past the sentries and turrets blocking his way.

"Omega?!" Shouted Rouge. "What's going on in there?"

"CASUALTY REPORT: ROUGE DEFEATED. SHADOW MORTALLY WOUNDED."

"What the hell is happening to him?" Shadow yelled over the din of battle around him.

"UNIDENTIFIED SYSTEM INTRUSION. EMERGENCY WITHDRAWL. MAIN SENSORS FAILING. I AM E-123 OME-" The transmission abruptly cut off in a burst of static, and Shadow watched as a burning and badly damaged Omega rocketed out of the hangar above him, flying away over the facility below and out over the dark hill country surrounding it, until the robot could not be seen any longer.

"Omega made it out." Shadow reported back as he watched his teammate flee. "He flew off to the east, but he looked like hell. I want to know what happened to him."

"Be careful Shadow. I have a bad feeling about this."

"I'll be fine." He grunted as he reached the hangar, dropping into a defensive stance as he studied the room's only other occupant.

It was an unknown creature, perhaps a canine of some sort. He was dressed in black, with a pointed silver mask on his face and a strange glowing object on his chest. When he spoke, it was in a deep and malignantly distorted voice, filled with scorn.

"Ahhhhh. Still more wonderful. Another guest. Not-so-tall, but just as dark and perhaps a bit more brooding than the last. Welcome, Shadow."

Shadow simply glared at the stranger in response. _Just my luck. Another lunatic with a big mouth._ "What did you do to Omega."

The stranger remained inscrutable behind his mask. "The world's most powerful robot? He was no more a challenge than crabmeat. My power is without peer, it is the ultimate strength!"

"And what power is that?" Shadow questioned with a raised brow.

"It is mine, and not for you to concern yourself with. Come now Shadow, our long awaited reunion, and yet you focus on such frivolous topics."

"I don't know you. And the only thing frivolous around here is that big mouth of yours."

The stranger laughed then, an undeniably disturbing sound that carried on far longer than Shadow cared for. "Ah, I suppose you would think so. I have changed much since our last encounter. Do you not remember the night you raided the Doctor's facility in the White Jungle? When you effortlessly destroyed a squad of jackal mercenaries, and then taunted their leader for his weakness?"

Shadow frowned as he remembered the night. The mission hadn't seemed to be anything out of the ordinary at the time. The jackals the stranger spoke of had been no more than cannon fodder for somebody as skilled in combat as Shadow was. Their leader had tried to attack him, and was taught a lesson for it. He had left the bruised and beaten jackal with an insult: " _Worthless. Don't show your pathetic face around here ever again_." Was this stranger that same being?

The ebony one's recollection was interrupted when the stranger spoke again. "Ahhh, I forget. You don't have the most accurate memory, do you now Shadow?"

The hedgehog in question growled at the insult and responded. "I remember you. I remember how easy to defeat you were."

The stranger simply laughed again. "Yes, I was a weakling back then. A weakling who thought he was strong. But you, Shadow, you showed me true strength. That night I gave up the right to my own face. I donned this mask and I let go of the old me, the weak me, so that I could become stronger. And in time, I obtained the power to make all yield to my will! I was reborn! I am now Infinite, and I am not weak!"

Shadow could only stare. _I should have just killed him. It's obvious he didn't take that defeat very well._ His musings were interrupted as Infinite clenched his fists and spoke yet again.

"I am what I am because of you Shadow. You showed me my weakness, but now I will show you my strength!"

With that, he unleashed a wave or red energy from the object on his chest. Shadow closed his eyes and braced himself as the wave struck him head on, yet it felt as if nothing happened. When he opened his eyes however, he was no longer in the hangar. Instead, he was back out in the hill country, in broad daylight. All around him floated trails of cubes made of the same odd glow as the stone in Infinite's chest. A few feet away, lay the broken body of Omega, with Rouge standing next to it.

Shaking his head, Shadow ran over to his ally's broken form and gazed mystified at Rouge. "How did you get here? And where's that guy? Where's Infinite?"

Rouge looked at him like he had gone crazy. _Maybe I have._ He wondered distantly.

"What are you talking about Shadow? We're here to pick up Omega, it's been three months since he was destroyed."

"Three months?!" He shook his head violently, starting to feel a headache. "What's going on? What are these cubes floating around?"

"Floating cubes? Rambling about nothing? Maybe you should see a doctor Shadow." Rouge said with a laugh.

"LIFEFORM SHADOW IS MALFUNCTIONING." Shadow started as Omega suddenly appeared, perfectly intact, next to Rouge. He looked to where the robot's broken shell had lain before, and saw nothing but grass there.

"Omega?" He asked weakly. "But you were destroyed..."

Rouge laughed again, as Omega responded. "NEGATIVE. I HAVE NEVER KNOWN DEFEAT. I AM NOT WEAK. I AM NOT WEAK. I AM NOT WEAK. I. AM. NOT. WEAK."

Shadow fell to his knees as his headache erupted into a migraine, covering his ears as Omega's voice grew louder and louder, sounding more and more like Infinite with every word. The pain in his head became unbearable and the voice in his ears was a constant roar. He collapsed to the ground with his eyes shut and screamed.

* * *

At once, everything was quiet. His head throbbing, he got to his knees and opened his eyes to look around. He was back in the hangar. Infinite was staring at him wordlessly.

"What. The hell. Was that." Every word was an assault on his throbbing head, and he could barely force himself to stand.

"That, Shadow, was true strength. _My_ true strength. I didn't know if you'd manage to survive, but you must admit, it was a wonderful show!" The jackal laughed again, and the sound of it forced Shadow back to his knees with his hands over his ears. "This power! Before we've even tuned it! Not even Sonic stands a chance against me now!"

"S-Sonic...?" Muttered Shadow. "What... are you... plotting?"

"Oh, Shadow. You'll see soon enough." With that, the jackal raised a hand and Shadow was sent flying backwards out of the hangar, and into the darkness. He was flung far away from the Doctor's facility and over the hills surrounding it. He barely had enough presence of mind to grasp the emerald from his quills and use chaos control to prevent a hard impact with the ground that likely would have given him another bout of amnesia.

Exhausted, head pounding, and confused beyond all measure, Shadow collapsed on the moonlit hillside and let unconsciousness overtake him.

* * *

 **Author's Note: This chapter turned out a lot longer that I initially expected. Oh well. I realize that some people don't like Infinite's origin story, but it was funny in a way and I honestly enjoyed it. I just decided to tweak a few things and make it a bit more real. "I am not weak" was just too much fun to throw out though. :)**

 **Reviews, suggestions, and opinions are always welcome, and hopefully I can get the next chapter out within a few days. Thanksgiving plans might slow it down a little bit. Anyway, till next time!**


	3. Hero's Fall

**Author's Note: Here it is, the next chapter. It gets a little violent, so be warned.**

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Chapter 2 - Hero's Fall

* * *

A gentle wind moved through the air of Green Hill, carrying with it the scent of fresh verdure, fertile soil, and the fine mist scattered by nearby waterfalls. Palm leaves swayed lazily beneath a clear sky, and the waters of the lakes reposed tranquilly under the small ripples of their surface. Birds chirping, grass and trees whispering in the breeze, and the omnipresent roar of water rushing down the cliffs, all melded together in a simple yet beautiful chorus.

It was a beautiful day, and Sonic the Hedgehog was enjoying it. Having just finished an easy subsonic jog through the area, he had decided to sit down and appreciate the beauty of the place for a while. At home under the shade of a large palm, he dozed contentedly on the lush grass as nature lulled him into a deep rest. Life was good. But it was not to last.

A shrill beeping emitted from a small communicator on the hedgehog's wrist, and with a sigh, he raised his arm up to glance at the screen.

 _Tails. Last I heard, he was still in Westopolis for that science convention of his. I wonder what he's up to?_

Sitting up and shrugging his drowsiness off, Sonic answered the call and greeted his brother. "Hey Tails. How's the science fair going?"

"Sonic! We need you to get down here quick! Its Eggman!"

The urgency in the kit's voice was heard even through the communicator, and Sonic was on his feet in an instant.

"How bad is it?" He asked, quickly stretching his legs.

"Very bad." Tails reported, worry lacing his tone. "There are death egg robots here!"

Sonic stopped for a moment as that sunk in. "Death egg robots?"

"Yes! Multiple death egg robots, and hundreds of egg pawns!" Multiple explosions and the screaming of civilians could be heard in the background as Tails spoke. "Please hurry Sonic, I can't fight this on my own!"

"Hang tight buddy, I'm on my way!" Switching off the communicator, Sonic dashed north towards the city, a sonic boom echoing in his wake as he left the peace and tranquility of Green Hill behind him.

* * *

Tails dove to the side as a chunk of what used to be a wall flew past him. The scene around him was a disaster. Citizens of the city fled in terror as eggpawns marched through the streets, intent on crushing any resistance, and death egg robos left a trail of flattened structures behind them. Flames licked up the sides of buildings that were still standing, and the air was choked with the scent of fire, oil, and death. The sun shone down through the thick smoke, and cast a reddish glow over the besieged city, giving everything a hellish look.

Blue eyes stared absently as the fox stood back up, glancing around at the carnage and ruin brought about by Eggman. He was bruised and exhausted, with several cuts on his left arm and one on the right side of his head where he had been a split second too slow dodging a large piece of shrapnel. _I hope Sonic gets here soon. I don't think I can take much more of this._

A scream from a nearby girl yanked Tails' focus back to reality. Steeling himself with determination, he jumped at the eggpawn standing over her, and wrenched it's head from its body. Grabbing the girl's hand, he pulled her up, pointing her away from the battle and telling her to run away from the city. He watched her for a moment, then turned back around to face the next wave.

* * *

Meanwhile, Sonic was just arriving at the outskirts of the city. He slowed to a stop at the top of a hill, briefly surveying the current situation. Eggman's army was already halfway through Westopolis, leaving a trail of burning and demolished buildings behind them. Citizens were fleeing in droves and the few who were staying behind to try and help fight weren't amounting to much. Casting a quick glance at the large metal behemoths rampaging through the town, Sonic noticed immediately that they weren't exact replicas of the death egg robot he had fought in the past. They were in fact much bigger.

 _Oh Egghead. Give up already, will ya?_

Sonic shook his head at the scene, and launched himself down the hill. His legs became a blur and his hands curled into fists as he streaked towards the battle, emerald eyes wide and mouth set in a determined grin as the familiar rush of adrenaline poured through him.

The first eggpawn didn't even see him coming. Neither did the second for that matter. Or the third.

A streak of blue, a rush of wind, the fastest thing alive earned his name as he literally blew apart the robots in his path. Turning to one of the death egg robos, he catapulted himself into the air, curling into a ball and cutting through one of the behemoth's arms. Hitting the ground running, he trashed a few more pawns before turning around and jumping atop one of the still standing houses. From there he jumped onto the robot's shoulder, and curled into a spin attack before shooting straight through the head as it turned to look at him. Landing in a crouch on another roof, he smirked and dashed off towards the next behemoth.

* * *

The citizens left in the city watched with a bated breath as the blue blur shot through the first metal monstrosity, its ruined body collapsing backwards and landing with an impact that shook the ground. With hope rising in their hearts, they cheered their savior aloud as he rushed further into battle, and it was only a few moments later that a second behemoth crashed violently to the ground.

Tails watched the robots fall and cheered with the rest of the citizens, feeling relief and hope surge through him. He smiled, and with both tails spinning, he flew off to greet his brother and finish the job together.

Sonic had just sent a third behemoth crashing down when he caught sight of Tails flying towards him from above. Giving the kit a grin and a thumbs up, he slowed to a stop amid the ruins as Tails ladded next to him.

"How's it going buddy?" Said the speedster, noting the bruised and exhausted state of his little brother. "You look like you've had a bit of a rough time here."

"Better now that you're here." Replied the fox with a grin. "You were cutting it kinda close, though."

"Awww, come on. You know that's pretty much how I roll." Sonic ruffled the kit's fur as he looked to the remaining bots. "I think it's time we go find the Egghead. No way there's an attack this big without Eggman around to personally supervise it."

"He's here alright." Tails added. "I just saw him in the main square, unless there's another fat guy in a flying machine around here."

"Let's get going then!" In a flash, he took off towards the square with Tails following close behind, smashing through any bots that stood in their way. Moments later, they had arrived at their destination, and were facing off with the cause of all the carnage around them.

Eggman looked down from his perch in the eggmobile with a sinister grin, as the two heroes stood together defiantly on the dirty stone pavement of the square.

"Sonic! What a pleasant surprise." The doctor greeted sarcastically. "Why, it's been so long since I last saw you."

Sonic shifted his weight to one leg, tapping his foot as he smirked up at the villain. "Not long enough in my book, Egghead. Now are you gonna play nice and stop destroying the city, or do I have to get up there and beat some sense into you again?"

Eggman grinned deviously. "I'd like to see you try, rodent."

Sonic smirked, and dropped back into a ready position. He launched himself up at Eggman, only to be viciously knocked out of the air before he could reach the mad Doctor.

Landing on his hands and knees, the hero glanced up to see who or what had interfered with his attempted attack, and was somewhat shocked to see Shadow the Hedgehog standing there and glaring at him with arms crossed.

"Shadow? What are you-" He was interrupted as a second familiar figure jumped from the roof of a nearby building, its large horned and spiked body landing next to Shadow with a heavy thud.

"Zavok?!" _What in the world is he doing here?_

But before he could dwell further on the presence of the red zeti, a viscous watery form rose up from a storm drain only a few feet away. Glowing eyes materialized and looked straight at Sonic as he stood there slack-jawed, futilely racking his brain for a reason to explain why and how Chaos had suddenly returned.

 _What the hell is going on here?_

And then as if those three weren't enough, Metal Sonic flew in from above, landing with metallic clang to join the other relics of Sonic's past. _How did- wait, Metal here actually makes sense. More than the rest of them do, at any rate._

All four stood there between Eggman and the two heroes, without a word or a move to attack. Sonic stood there, blinking in the late afternoon sun as he looked from one former enemy to the next. Tails was busy trying to pick his jaw up off the ground, not having yet decided whether he should be confused or scared.

As the heroes studied the villains of their past, a fifth figure manifested itself, seeming to appear out of thin air in front of Sonic, who immediately stepped back into a defensive posture. The figure was clad all in black and silver, and stared out at the blue hedgehog from behind his mask, apparently waiting for him to make a move.

Regathering his composure, the cocky speedster looked up at Eggman again, then back at the ensemble of villains, before asking: "Is that finally all of them, or should I be waiting for another guy to jump down from the roof?" With that, he launched himself at the masked figure.

And ran straight through him.

 _An illusion?_ Sonic pondered as he skidded to a stop. The next moment a very real black gloved fist smashed into his gut, sending him flying back into a wall.

 _Owww._ Was all he could think as he shook off the impact, while Eggman cackled in delight. _Definitely not an illusion._

Tails, seeing his brother's plight, flew towards him but was blocked by Shadow. The fox hesitated for a moment, knowing that he wasn't a match for the Ultimate Lifeform, and Shadow took the opportunity to taunt him with a grin that seemed almost feral. "Too scared, fox boy?" A splot second later he roundhouse kicked the outclassed kit into a telephone pole.

Sonic watched Shadow send his little brother flying, and with a growl he leapt away from the wall he had been knocked into, charging at the ebony hedgehog with fists raised. But he didn't get far, as Metal shot towards him from the side and he was forced to roll out of the way. Then Chaos was suddenly in front of him and he only just managed to raise his fists fast enough to block two watery appendages targeting his face. While he was busy fending off the water-god, Zavok's fist suddenly connected with his side and he went flying into another wall with enough force to shatter it.

Groaning out loud, he shakily stood up again. _This isn't going too well._ He realized with not a small amount of trepidation.

"Tails!" He called to the battered fox, who was only just getting back to his feet himself. "Tails get outta here! Run!"

Sonic would have said more, but Metal appeared behind him and sent him flying again. Right towards the masked one, who kicked him up into the air. For the next few moments, pain prevented any kind of coherent thought for Sonic. Tails watched, frozen in mounting horror as the blue hero was kicked from villain to villain like a cheap toy, finally crashing to the ground in a bruised and dizzy heap. Eggman's grin at this point could only be described as satanic.

"R-run... Tails..." Sonic coughed weakly, struggling to get up once again, before being knocked unconscious by a merciless metal fist to the side of his head.

At once, all the villains turned towards Tails, who at this moment was more terrified than at any other point in his young life. Choosing to heed the last words of his brother, he turned and fled the scene, eyes choked with tears as Eggman's laughter echoed behind him.

* * *

For the first time in anybody's remembrance, Eggman stood unopposed as his robots marched through the rest of the Westopolis. The citizens who had witnessed the tearful retreat of Tails could only assume the worst, and with their hero defeated, their last hope for the future faded. As the sun dropped to the horizon, its last rays of light shone over a decimated city. The ruins were a blazing inferno overshadowed by clouds of smoke, and filled with the stench of destruction and death. A bruised, exhausted, and broken-hearted Miles Prower stood on the hillside overlooking the city, tears streaming down his face for his fallen brother.

 _What hope is there for the future now?_

* * *

At that very moment, in the wide open Mobian plains several hundred miles to the east, where only the faint remnants of twilight still remained in the sky, a portal opened. A white furred hedgehog fell through it, and landed in a crouch. He was on a mission, and he was prepared to go through hell to see it accomplished. That mission?

 _Bring hope to the future._

* * *

 **Author's Note:** **Apologies if this is a little darker than you were expecting. I feel like if you take the Sonic Forces story seriously, it is one of the darkest stories we've seen in sonic for a long time. Anyway, I changed a good bit with this portion of the story. I really don't like how SEGA have turned Tails into a cowering child who doesn't fight anymore. So I gave him a basic fighting role, at the least. If he's scared when facing foes like Shadow or Metal on his own, that's fine. He's pretty outclassed by them IMO, so he has a reason to be afraid. I just think it's a bit ridiculous to cower in fear before base form Chaos, and not try to fight or even to run away.**

 **Anyway... I hope you guys liked the chapter. This is likely to be one of the last chapters that stick at all close to the game storyline. From here things change quite a bit, with the Avatar/OC not having a place in this story and Shadow/Silver playing much more prominent roles. Some other things will be changing too, but I'm not going to spoil them here. :)**

 **As always, reviews/suggestions/opinions are welcome, and I'll be back with the next chapter hopefully within a few days.**


	4. Too Late?

**Author's Note: Alright, chapter 3 is here folks!**

 **Thank you all for the interest and support you have shown for this story.**

 **hellbentstar06** **\- Absolutely, feel free to take whatever ideas or pointers you want for use in your own fic.**

 **Mitha Sentro - Sorry to disappoint, but Blaze will not appear in this story. I wrestled a lot with whether or not to include her, but ultimately I decided against it for several reasons. I dont really have a lot of experience with Blaze, and I don't think I could do justice to her character here. I also don't know which of her backstories I would adapt for this. The biggest reason though, was that I already have a wide cast of characters here, and I feel that including Blaze would detract a lot from Silver's story and his interaction with the others.**

 **King Needlemouse - Some major plot points from the game will stay the same, with little to no changes, but there will also be a lot of new twists and turns in periods that the game just kinda glossed over.**

 **Libra-no-ninja9 - Yeah, this definitely isn't a fun period for Tails. And I promise, you'll see what Shadow is up to soon.**

 **But anyway, without further ado...**

* * *

Chapter 3 - Too Late?

* * *

A cool wind rolled over the darkened plains as a glowing portal opened above the grass, allowing a pale figure to drop through. As he landed in a crouch on the ground, Silver the Hedgehog shook off the mild disorientation caused by his passage through time, and took stock of his surroundings.

Wide open flatland stretched out all around him, with nothing on any horizon except the faint outline of distant a mountain range in the west, silhouetted against the last remnants of twilight. He glanced up at the unclouded sky above, filled with the twinkling of thousands upon thousands of stars, and could only stare up at it in wonder. His future home, ruined as it was by flame and pollution, rarely offered a view such as this. He trailed his hands through the tall green grass stretching up to his waist, as he slowly wandered through the new and unfamiliar environment. Comparing the simple beauty of this place with the desolated wasteland that was his home filled him with a strong determination to prevent that future from ever coming to pass.

That was much easier said than done, however. The chaos control he had induced to get here was rather unpredictable when used on such a scale, and he didn't know exactly where, or even _when_ , he was. He could only hope he had traveled far enough back to prevent whatever defeat had been suffered by this _Sonic_ character referred to in the document.

As he turned towards the distant mountains, setting off at a brisk run, Silver's thoughts turned to the ancient parchment tucked into his quills. It had been discovered only a few months before he was sent on this mission, under most unusual circumstances. The ruined condition of the planet had for centuries been causing the polar ice caps to melt away, and what little remained during Silver's time would not last for long. It was there, amid the ever receding arctic glaciers, that the scavengers had discovered the island.

It was a large rocky mass, strewn with the frozen remains of a tropical ecosystem, unexplainable by any natural phenomenon. Weeks of excavation revealed a number of ancient stone ruins, bearing inscriptions written in a language that had long since been lost to the world. The most significant of these ruins was a large stone shrine, obviously designed to hold something of great value. It was at the top of this empty shrine that the parchment had been found, sealed along with a single chaos emerald inside a wooden chest that had by some miraculous circumstance preserved it from the centuries of ice and damp.

Unlike the inscriptions elsewhere on the island, this document was written in plain language, and while not everything that it spoke of made sense, enough was gleaned from it to piece together an idea of just how the world had started down its path to ruin. And with the cause of ruin discovered, a desperate plan was hatched to prevent it.

* * *

Just before daybreak, Silver reached the top of the mountain range he had seen upon his arrival in this time. He stopped here, deciding that this was a good place to take a rest and catch his breath after running all through the night. Sitting tiredly on boulder at the top of one of the peaks, he looked back at the wide open plains he had come from, just being lit by the first rays of the rising sun. The absolute _greenness_ of it was astounding to the hedgehog. Tearing his eyes away from the beautiful sight, he looked out to the west. It was still covered in the long shadows of the mountain range he sat atop, but a brightening sky revealed the high peaks steadily dissolving into small foothills, which gave way to a level plain that eventually dropped into the ocean near the horizon. Not a cloud was in sight, except for a distant grey pall that rose up over an area near the coast.

 _Wait a minute._ Thought Silver. _That's smoke! And a lot of it! Where there's smoke, there's fire, and if I'm to find this hero, a fire this big seems like a good place to start looking._

With all traces of exhaustion forgotten, the white hedgehog raced down to the west, eager to reach the source of the conflagration. Time passed he drew closer, and with the steadily climbing sun's rays behind him, he could make out the outlines of ruined and collapsed buildings under the smoke, along with a dark mass off to the south of the disaster scene.

Upon closer inspection, that mass was revealed to be a slowly traveling throng of what he presumed were evacuees. Leaving the burning city to its fate, he turned towards the crowd ran faster, hearing their sounds of mourning and weeping carry through the air. Women were weeping as they carried their wailing children across the landscape, and ashen faced men carried sacks of belongings and provisions, staring down at their feet as they treaded onward. The entire crowd was pale, covered in soot and ash, and some were bleeding from various injuries. The hopelessness and defeat radiating from the scene were palpable, and Silver was frozen on his feet for a few moments after he arrived on the scene, staring helplessly at the throng. It looked like a crowd of the dead, endlessly walking in the pale morning light without either destination or hope.

Finally getting his feet to move, Silver approached the nearest of the refugees, a female bird carrying a restless young girl in her arms. "What's going on here?" He asked. "What happened?"

She looked to him with a woeful expression. "It's over now. There's no hope for any of us after today." With a despairing shake of her head, she continued past him. The next several people he asked didn't even respond, a few managing a shake of their heads as they all stared hopelessly at the ground.

With a growing pit in his stomach, Silver approached a male dog, bleeding slightly from a cut on his head as he carried a large sack over his shoulder. "What's going on here? Please, I have to know what happened."

With a despairing huff, the dog pointed behind him at the rear of the group, saying with a resigned tone: "Ask him."

Silver looked where the dog was pointing, and saw a lone young fox, trailing far behind the rest of the crowd. His head was bowed down, and he walked with heavy steps, tears dripping from sky blue eyes as he aimlessly followed the retreating throng. Twin tails dragged along the ground behind him as Silver slowly approached him and, with the most gentle tone he could muster at the moment, asked: "What happened?"

The fox didn't even look up as he answered, his voice filled with despair and grief. "He's gone. My brother is gone. What am I supposed to do without Sonic?"

Silver's blood ran cold as the kit voiced his brother's name, the name of the hero spoken of in the document. _It can't be. I can't be too late! He can't be gone already!_

"Sonic... the hero?" He questioned weakly, almost fearing the answer.

The kit sniffed, and nodded once, too choked with tears to speak more.

Any other time, Silver would have tried to comfort the poor fox, but right now he was having a mild panic attack. _No! How could I be too late?! Why? It can't end like this, it can't! Never give up Silver, Never!_

He managed to put a comforting arm around the fox, before asking "How did it happen?"

"W-we were fighting Eggman, l-like we always do..." the young two-tail answered through his tears. "B-but Eggman... Sh-Shadow..." the words trailed off into muffled sobs. The kit took a deep breath, and in an emotional rush he cried: "He told me to run, and I did! I ran and I left him for dead with Eggman and his goons!" With that he collapsed onto the ground, curling his tails around himself as he sobbed uncontrollably.

Silver sat next to him, putting an arm around him and taking the time to analyze what had been said.

 _Eggman. That's another name from the document. The name of the first emperor._ Gloved hands fisted and his mouth twisted in a grimace. _He's the one to thank for the planet's ruin. But where do I go from here? Sonic is already gone, how can I prevent what I know has already started to happen?_

Shaking his head, the hedgehog reached behind him to pull the ancient document from his quills. Perhaps reading through it again would give him an idea or two. He had almost forgotten about his company until a quiet voice from his side asked: "What is that?"

Freezing in surprise, Silver stared like a deer in the headlights at the sad young fox next to him, who had calmed down and stopped crying as Silver sat next to him. "Uhhhhhh... Nothing?" He said nervously, shoving the parchment back into his quills. He didn't think this kid would do anything bad with the document, but he wasn't sure that explaining his whole mission to somebody he just met was a good idea. The fox, however, wasn't going to give him a choice in the matter. "What do you mean nothing?" He said, managing a weak glare. "I saw Sonic's name on that paper! Who are you?"

Silver sighed as he pulled the document from his quills again. "It's... a long story." He handed the parchmemt to the fox, keeping careful eye on it as dirty gloved hands unrolled it and blue eyes quickly scanned it.

The kit's breathing grew shallow, and his face went even more pale than it already was. "W-where did you get this?" He asked in a trembling voice. Then something clicked in his mind, and he turned to the white hedgehog with a suspicious look. " _When_ did you get this?"

Silver was amazed at the fox's keen intuition, even through his grief, and stared levelly at him as he answered: "My name is Silver the Hedgehog. I'm from over 400 years in the future, where the planet is ruined and life is only hanging on by a thread. That parchment was found in a chest in an ancient shrine on a frozen island in the arctic glaciers, and I'm here to prevent what it refers to, the defeat of the hero Sonic the Hedgehog. Only... it seems I'm too late..."

The fox stared at him, his grief taking a back seat as his mind worked feverishly, staring back and forth from the document to Silver, then back again. Then he stood up, staring at the future hedgehog with a determined look on his tear-stained face. "I'm Tails. Sonic was... is... my brother, and he wouldn't want me to give up like this. We need to take this document to Angel Island. There's somebody there who will be able to help us."

"Angel Island? Somebody to help us? What?"

"You said you found this on an island, in the arctic glaciers?"

Silver nodded.

"I know where this document came from, and I know who wrote it." Said Tails in an urgent voice. "Come on, we have to find a plane or something that can get us in the air!"

"How far away is this Angel Island? Couldn't we just use a boat to get to it instead?" Silver wondered out loud.

"No, Angel island floats through the sky." Tails answered, like it was a completely normal thing for islands to fly.

"Come again?"

"Just come on and help me find a plane!" The fox grumbled as he started walking back towards the ruined city. "I hope there's still one intact..."

"Actually..." Silver interrupted, aqua circles on his hands and bracelets glowing as he rose up into the air. "I can levitate us there, as long as it isn't extremely far."

Tails gaped at him for a moment, before responding. "Awesome! It's a few hundred miles off the coast right now, and about 30,000 feet up..."

The hedgehog smiled. "I can manage the two of us that far. Let's go!" Hands stretched out, a cyan glow surrounded them both as Silver levitated them from the ground.

Tails smiled in wonder at the future one's powers, and Silver was happy to see the young kit's face without grief, if only for now. With a burst of power, he impelled them both towards the coast, leaving a sonic boom in their wake

* * *

Within an hour, and with some guidance from Tails, they were within sight of Angel Island. Floating above the clouds, peacefully floating on nothing but air, the lush tropical paradise was unlike anything Silver had ever seen. An impossibly green mass, with several mountain peaks sticking up from its center, and streams of clear water flowing off the ledges. Landing on the island, some 30,000 feet in the air, Tails immediately headed off into the jungle. Silver however, never having seen a floating island before, couldn't resist peeking down over the edge to see the clouds and ocean below, before following the fox into the thick vegetation.

A narrow trail lead them through the verdure, winding its way deep through the jungle and into the heart of the island. There, nestled between the spurs of the mountains, was a large ancient stone shrine. Silver gasped in recognition. _That's... the shrine where the document was found! Will be found? Has it even been written yet? Time travel is so confusing sometimes._

As the two reached the foot of the shrine, and were about to set foot on the steps leading to the altar above, they found their path suddenly blocked by a very red, very tough looking, and very _angry_ echidna.

"Tails! Who have you dragged here now? My island is _not_ a tourist attraction!"

* * *

 **Author's Note:**

 ** _"Here I come, rougher than the rest of them,_**

 ** _the best of them, tougher than leather..."_**

 **I can't be the only one who wants character theme songs to come back.**

 **Anyway, I hope you guys enjoyed the chapter. Less action in this one, and more setting up the later story. Now we're embarking on the six month period after Sonic's defeat that the game story completely glossed over. I know there are probably more questions about the document that I keep referencing, but they'll all be answered in due time.**

 **Even though this chapter** **focuses more on Silver, I hope I did alright with Tails, as he was the more challenging here. Starting off as a wreck because he just lost the most important person in his life, but then calming down and being distracted from his grief by a new purpose, so much that he's the one who helps Silver figure out what to do now.**

 **As always, review/suggestions/opinions are welcome, and I'll be back with another chapter in a few days.**


	5. Birth of the Resistance

**Author's Note:  
**

 **Thank you again to all my wonderful reviewers.**

 **King Needlemouse - To be honest, the game didn't have much story to it at all. Six months while Sonic was imprisoned, they just ignore and gloss over. So while I'm definitely going to keep elements of the game's plot, there is going to be a lot of material in this story that will be completely new, because there's just so much that the game didn't cover.**

 **Guest102 - Thank you for your kind words. I hope you enjoy the rest of the story just as much!**

 **MobiusHero - Thank you for your support and your suggestions. I do plan on making chapters a bit longer now that we're really getting into the story. This one is over 4,000 I believe. And as for what I'm going to do with the villains, you'll just have to wait and see. :) I'm not going to completely get rid of the game's plot, but I think you'll like the way I tweak it and expand upon it.**

 **And without further ado...**

* * *

Chapter 4 - Birth of the Resistance

* * *

The air was cool and thin as it swirled lazily through the tropical forests of Angel Island, carrying nothing but the aroma of fresh verdure and the faint scent of the salty sea spray thousands of feet below. This island, with its unique and tragic history, was home to but a single inhabitant. Last of his kind, he was eternally bound to the floating mass, destined to forever guard the great and powerful secret enshrined therein. It was a solitary and lonely life, but the guardian had accepted his fate long ago. The sacred duty of guarding the Master Emerald was all that remained of his past and his culture, and he would faithfully perform it until his last breath.

So it was that Knuckles the Echidna, guardian of the fabled Master Emerald, awoke from a nap at the foot of the Emerald Shrine one afternoon with the unpleasant feeling that there was a stranger on his island. It was an uncommon feeling, but one that he recognized easily. As guardian, he had a unique and powerful connection to the large gem, and since its power was so infused throughout the entire floating island, he had a limited ability to sense whatever was happening on it. And right now, there were two beings traveling through the jungle, headed right toward the Emerald Altar.

Growling in annoyance, Knuckles stood and walked up the ancient stone steps of the shrine to stand before the emerald. Closing his eyes, he reached out toward the glowing gem and tapped further into the bond he shared with it. As he sunk deeper into his connection with the emerald, he received the vague impression that there was something off in the world below, something unusual and almost foreboding. Shrugging the feeling off, he focused more on the presences he felt intruding upon this secret hideaway. One was almost immediately familiar. The young, honest, and virtuous soul of Tails was easily recognizable, and while the echidna never truly _welcomed_ anybody to his island, the kit would undoubtedly be treated with much more leniency than others would be.

The second presence, on the other hand, was a mystery. It was unfamiliar, different from the other presences he had sensed in his lifetime on the island. It wasn't the whirlwind of life and feeling that represented Sonic, nor the calculating and scheming mind of the evil doctor who had been his first contact with another sentient being. It was guarded and focused, yet also tinged with amazement and curiosity. Whoever it was, Knuckles had not met him before.

 _So why is Tails here without Sonic?_ The guardian questioned mentally as he pulled back from his connection to the emerald. _And why did he bring a newcomer here? He knows better than to go around telling people about this place!_

The questions would be answered soon enough, he supposed. Even now he could feel the two getting close to the shrine. He crossed his arms and stood quietly for a moment in the peaceful afternoon sunshine, waiting for the interlopers to arrive. Shadows were just starting to lengthen as the sun began its slow descent into the west, and as Knuckles continued to contemplate the unfamiliar stranger who was accompanying Tails, that odd sense of abnormality and foreboding he had felt before returned.

His sharp hearing picked up the rustle of leaves and the tread of footsteps from the jungle at the foot of the shrine. Leaping down from his perch at the top of the altar, Knuckles landed with clenched fists and scowling face in front of the trespassers. Tails was startled for a moment, but recovered easily, having seen much worse from the guardian in past meetings. The stranger however - a white hedgehog with golden eyes and bracelets covered in cyan markings - was unfamiliar with the guardian. He stepped back into a defensive posture, raising his hands and surrounding himself in a cyan glow that matched the markings on his gloves and bracelets.

A decade ago, Knuckles probably would have charged ahead and attacked the stranger without question. Time and experience however, had taught him to try using his head before his fists. His scowl set upon the young fox who had brought the hedgehog here, the echidna sought for an explanation.

"Tails! Who have you dragged here now?" He demanded with a gesture toward the newcomer. "My island is _not_ a tourist attraction!"

The fox quickly moved to stand protectively in front of the newcomer. "He's a friend!" Tails shouted, in a rather hoarse voice that betrayed how tired and emotionally worn he was. Then in a softer voice he added: "We need your help Knuckles."

As the kit spoke his name, the white hedgehog gaped and stared closely at the guardian. "You- You're Knuckles?" He asked in wonder.

Knuckles grunted, and rejoined: "What's it to you?" Then he turned back to Tails, who was covered in various scrapes and bruises, and looking decidedly worse for wear. "What happened to you, and why do you need my help?" Glancing back at the hedgehog, he thought of a better question. "And where's Sonic?"

The stranger shook his head, and Tails looked close to tears. The foreboding feeling in the guardian's gut intensified into a knot of worry and fear, and he repeated the question. "Tails. Where is Sonic?"

The young fox couldn't hold it in anymore, with his mind replaying the memory of his brother's terrible fate. Tears began falling from his eyes, and in a broken voice he cried: "H-he's gone... Eggman..." He sobbed. "E-eggman defeated him, and I.. I don't even know if he's still alive!" Unable to speak more about the subject, Tails bowed his head and covered his face with his hands, sobbing aloud.

With a somber look, the white hedgehog moved closer to Tails, wrapping a comforting arm around his shoulder. Knuckles however, hardly took notice. Instead, violet eyes stared blankly ahead as his mind worked to make sense of what he had just heard.

 _Sonic defeated?  
_

The guardian was not a very open or emotional being, but even so, he considered the blue hedgehog to be a close ally and friend. To hear of his defeat... It was jarring, to say the least.

Knuckles had fought Sonic in the past, and he had been on many adventures as the hedgehog's ally. He had witnessed for himself what the blue blur was capable of, and he knew Sonic was never one to give up the fight. So what kind of evil machination was it that could have defeated fastest thing alive? There had been close calls in the past, like the Perfect Chaos or ARK incidents, but the cocky hero always seemed to pull through no matter what.

He glanced again at Tails, who had composed himself somewhat by now, and then to the unfamiliar figure standing next to him. There were more questions that needed to be answered, but the narrow jungle trail they were standing on wasn't the best place for a lengthy discussion. "Come with me." Knuckles declared, turning to lead them up the stairs of the shrine. Upon reaching the top, he walked over to the small chest of provisions he kept next to one of the crumbling pillars, pulling out a flask of water and handing it to Tails. He pointedly ignored the stranger's gaping stare at the giant glowing gem sitting in the middle of the altar. Moving between the emerald and his guests, Knuckles gestured to both of them and said: "Sit down."

In a moment, all three were resting on the worn stone floor of the altar, in the warm afternoon sunlight with a cool breeze sweeping over their skin. Silence reigned for a few moments, as Tails tipped the flask and drank a few sips. The guardian watched silently, noting again the exhausted and bruised condition of his friend, and waiting for him to speak. Setting down the flask, the fox took a few deep breaths, before turning to face Knuckles with a new life in his sky blue eyes.

"Thank you Knuckles." He said, receiving a small nod in response. Then he gestured to the unknown visitor, announcing: "This is Silver the Hedgehog. As for why he's here, it's kind of a long story, even I don't know it all yet."

The golden-eyed hedgehog nodded, and reached back into his quills to produce a thin parchment, which he then held out to the echidna.

"Before you ask anything else, you should read this."

Knuckles warily took the paper, which proved to be a handwritten document of some sort, and violet eyes quickly scanned it. His face quickly grew pale and he read it a second time. Then a third. The words he stared down at - words written _in his own handwriting_ \- shook him to his core.

* * *

 _To whom it may concern,_

 _This is the final account given by the last guardian of the Master Emerald._

 _I'm sorry that I failed you all._

 _I should have been paying more attention, but chained to my duty up here on this island, I left my friends alone when they needed me the most. I probably couldn't have changed anything, but dying with them all then would have been preferable to this.  
_

 _It's been 7 months now, since Sonic was defeated. Even now it feels so wrong to say it. Sonic the Hedgehog, hero and defender of Mobius, defeated by a mad tyrant. He faced down and triumphed over so much evil during his life, he was an unstoppable force for good in this world... It just seems so wrong for it to end like this, with Sonic dead and Eggman sitting on a throne ruling his long-awaited empire._ _But no matter how wrong it seems, he's still gone. They all are. I didn't even know anything had happened until weeks later, and by then it was too late. I don't know how it happened to most of them, but my friends and allies are all gone now. It's odd... I rarely appreciated their company when I had it, but now that they're all gone, I feel more empty than I ever have before._

 _I've spent the last 6 months trying to keep the Island hidden. Influencing the emerald to fly through storms and cloud fronts in an effort to keep "His Imperial Majesty" guessing. It's worn me down, and I know I wouldn't be able to keep it up for much longer. There's no hope anymore. With Sonic gone, nobody has the strength or will to oppose Eggman. Sooner or later he would find me, he would find the emerald, and I would be too weak to stop him. I would fail in my duty as a guardian._

 _I cannot let that happen, so I am taking the last option I have. I'm going to take the emerald out of it's place and leave my island to it's fate. I'm going to hide the emerald away from the world permanently, and then I'm going to leave it. The only way to protect it is to leave it, and hopefully draw Eggman away from it._

 _As Knuckles, to anybody who still knows me by that name: I'm sorry I failed you all. I'm sorry I left my friends to die without me. I wasn't there when you needed me the most, and not a day goes by that I don't feel terrible for it._

 _As final guardian of the Master Emerald, to anybody who seeks it after I'm gone: It's not here. By my life, by my death, nobody will misuse the Master Emerald ever again._ _I'm going to hide it away forever, and then I'm going after that evil madman. I probably won't last a week, but that's ok. My friends are all gone, and once the emerald is gone too, there won't be any purpose left for me in this world. I'm going to throw everything I've got at Eggman, and then in the end, maybe I'll see my friends again._

* * *

There was nothing more to the document except for a small signature, and a date written in the bottom corner. That date was exactly 7 months away, and as he stared down at the familiar handwriting, Knuckles couldn't help but feel slightly nauseous. His friends all gone, the emerald in peril, Eggman ruling an empire? It was terrible to imagine. Even more terrible was the knowledge of how it would all end. The guardian suspected he knew what his future self planned to do. It had long been one of his last contingencies to hide the emerald if there were no other options. _Could it really be true?_

He jerked his head back up toward Silver, narrowing his eyes. "Where did you get this?" He demanded roughly. "And where are you from?"

Silver held his gaze. "I came here from the future." He said levelly. "Over 400 years in the future. In my time, the planet is a polluted wasteland, covered in ruins and fires and machines. The legacy of Eggman's empire." He shook his head before continuing. "We found that document, along with a single chaos emerald, right here on this shrine where that emerald is sitting. Only the emerald wasn't there, and this whole island was sitting in the middle of a melting arctic glacier. I came here to prevent that future from ever happening."

Violet eyes stared intently into golden ones as the explanation was voiced. Silver never looked away, nor did his voice falter. Failing to perceive any trace of deceit in the white hedgehog's bearing, Knuckles sighed and looked back to the document in his hands. _In the glaciers. So I actually did it. Crashed the island and sealed away the emerald, and then took on a suicide mission against a tyrant. Not how I thought I'd go out.  
_

Sometimes, the guardian really wished for the old days. Back when it was just him and his Island and the Emerald, no adventures and no time traveling and definitely no hedgehogs. This was something he couldn't avoid though. It was obvious from the letter that he couldn't sit this one out.

He lifted his gaze to Tails, eyes roaming again over the fox's bruised and tired body, and recalling the kit's grief over what had happened to his brother. _Even if I could sit this one out, I don't think I'd want to. If Sonic really is gone, then Tails needs me now more than ever. And if Sonic is still alive somewhere, I owe it to him to do everything in my power to save him._

Stretching his hand out to give the parchment back to Silver, Knuckles stood up and walked over to the emerald, gently placing his hand on its glowing surface. "If what that paper says is true, then I can't just sit here like I always do." Looking to Tails, he said: "I'm going to help you fight Eggman, and if Sonic is still alive, we're going to find him. I promise you." Turning to Silver, he added: "We - all of us - are going to save the future. We're not going to let Eggman ruin the planet, and we're not going to let what's written on that paper ever happen."

Silver and Tails stood up as well, nodding in approval.

Knuckles continued: "With Sonic gone, Eggman is going to waste no time in expanding his empire across the globe. We have to move fast if we're going to stand a chance."

"We need to find as many friends and allies as we can." Tails piped up. "We can't do this alone."

"Nor should we." Silver responded. "We need to rally the people. We have to show them that there is still hope, they just have to fight for it!"

"First things first." Knuckles interjected. "We have to figure out how we're going to organize this resistance of ours. We need a well-hidden base to operate from, and I need to make sure the Master Emerald stays safe through all of this."

Tails looked at the Master Emerald thoughtfully for a few moments, then turned back to it's guardian with an apologetic look in his eyes. "I have an idea that would solve both problems, but you're not gonna like it."

The red echidna quickly caught on to what Tails was proposing, and his eyes widened. "No." He stated firmly.

"No to what?" Questioned Silver. He was ignored as the other two argued back and forth.

"Tails, I promised to help you however I can, but you can't ask this of me."

"Come on Knuckles, you know there's no better place than this. We all have to make sacrifices."

"Sacrifices? Sacrifices are one thing, but exposing Angel Island to everybody who decides to join our little fight-back club, that's entirely different!"

"If we chose any other place, you'll have to either leave the emerald here undefended, or take it with you somewhere else and leave the island to crash down and be overrun by Eggman's army!"

Knuckles just huffed and crossed his arms, turning his back to the fox. _You know he's right._ His thoughts taunted him. _But that doesn't mean I have to like it!_

Tails continued his pleading: "At least if we make our base here, we can all defend this place if we need to! And you know how to keep this island well hidden, you've been doing it for years! Please Knuckles, it's our best option."

The echidna growled in frustration, before throwing his hands up and turning back to the kit. "Fine. On one condition."

"What?"

"If we make our base here, I'm in charge. Nobody gives me orders on this island, and I will make decisions as I see fit. I'll take the emerald to Hidden Palace, where it will stay off limits and a secret to everybody who joins our resistance here except me, understand?" _If I have to give up the secret of this island, then I'm at least going to do it my way._

Tails thought for a moment, before nodding his head. "Deal. As long as you promise to at least take our advice and opinions into account when you're making important decisions."

Knuckles nodded his assent, and turned to Silver, who had been watching the exchange with interest. "That good with you?"

The future hedgehog shrugged. "I certainly don't have a better idea."

"Its settled then." The guardian pronounced. "Our resistance can use Angel Island as a hideout, but I'll be the one making the decisions. Now Tails, before we start heading out to find allies and fight back, we need you to tell us everything you know about Eggman's new army and how he managed to defeat Sonic. We have to know what we're up against."

Tails nodded slowly, and started to recount what he knew. "The army is bigger than anything we've faced before... Eggpawns were as countless as sand on the beach, and there were at least a dozen giant death-egg style robots as well. The biggest mass-produced mechs I've ever seen. But if it were only that... Sonic would still be here." Tails took a shaky breath as he continued describing the painful incident. "We tried to reach Eggman, to make him stop the attack... But he had a team of our past enemies waiting for us. A very odd assortment of characters, which still doesn't make sense." He looked over to Knuckles. "Chaos was there."

"What?!" The echidna cried out.

"Chaos was there." Tails repeated. "He was there in his base form, along with Shadow, Metal Sonic, and Zavok, one of the Zeti we faced during our adventure on the Lost Hex. And then there was also a new enemy. A masked figure with a power unlike anything we've seen before."

"None of that makes any sense!" Growled Knuckles. "Metal Sonic, fine. But everyone else... How? Why? I should have known if Chaos was roaming the planet again, but there wasn't any sign from the Master Emerald at all!"

"Who are all these people?" Interjected Silver, mildly embarrassed.

Tails only shook his head, gingerly sitting back down on the the ancient stone beneath him, wincing as his bruised body protested at the movement. "It's a long story..."

* * *

Shadows lengthened and the air grew cooler as the next few hours were spent explaining the history of the odd cast of villains they were facing, and trying to figure out a logical explanation for why some of them were there at all. The presence of Chaos was a frustrating mystery that no clues or theories were able to help explain, and none of them had the slightest clue about Shadow's motives. "The idiot probably got amnesia again and forgot he was a good guy." Knuckles had grumbled at one point. Zavok's presence was equally mystifying, and the only plausible explanation was that Eggman had somehow gone back to the Hex and allied himself with the zeti, before bringing the red monster back down with him so both could get revenge on Sonic. And as for Metal Sonic, well, it actually wasn't very hard to guess why or how the robot was there. Especially compared to the rest of the odd assemblage.

As for the new figure among the familiar villains, nothing was known about him. Not his name, not his power, nor where he had come from. He was a mystery greater than all the others, and one that could not be solved without much more information, which would probably be quite difficult to get.

The trio discussed these villains, and potential plans to fight back against them, as the sun dropped lower and lower over the western horizon. Darkness was gathering quickly on the island when the trio finally decided to call it a day.

"I think further discussion and planning will have to wait until morning." Knuckles said as he stood up, stretching. "Light will be gone soon, and I know we could all use some sleep before tomorrow." _Some of us more than others._ He added silently, glancing at Tails.

Silver nodded appreciatively as he stifled a yawn, having been up and running since long before dawn. He stood up and held a hand out to Tails, helping the bruised kit stand up, before following Knuckles as he turned and headed down the steps of the shrine. They followed him for a few minutes as he walked along one of the jungle paths leading away from the shrine, before reaching a small clearing. A hammock made of vines was strung up between two of the trees, and there were a few provisions scattered about the area. Tails was given another draught of water and use of the hammock, while Silver reposed on the grassy turf below and Knuckles leaned back against a tree trunk.

They all settled in for the night as twilight faded to the west. Tails fell asleep quickly, his body eager for rest and recuperation, but Silver and Knuckles lay silently awake for a while. Silver's mind was abuzz with everything that had happened to him since he had arrived in the past less than 24 hours ago. Seeing the still untarnished beauty of this past world, meeting Tails amid the refugees fleeing a ruined city, learning about the enemies facing him on his quest to change the future, and finding allies to help him along the way. He knew this would be a hard struggle, especially with Sonic already defeated, but Silver had already vowed never to give up. With spirit and perseverance, no matter what the obstacles, the white hedgehog had faith that they could see this through to the end. Knuckles, meanwhile, couldn't help but feel foreboding in his heart, as he thought about the struggle that awaited them in the coming weeks and months, and about the terrible future described by Silver and his document, which would inevitably come to pass if their resistance should fail. Thoughts of what had happened to Sonic, worries about the safety of the emerald, and uncertainty regarding the upcoming war, all weighed him down as he drifted off to sleep. But even in sleep he couldn't find an easy rest, troubled through the night by dreams of a not-so-distant and ruined future.

* * *

 **Author's Note: Alright. We've got our resistance. Kinda.  
**

 **Anyway, I took a little bit of liberty there with Knuckles connection to the Master Emerald allowing him to sense what's happening on Angel Island. His connection to the emerald is cannon, yes, but I decided to expand that somewhat. The emerald is what keeps the island afloat, so I figured that it would be plausible for Knuckles to sense things on the island to a degree, and also to influence the emerald to "fly" and steer the island itself.**

 **Also, the game doesn't explicitly tell us where that little resistance HQ is. So I chose Angel Island, because it's well hidden, because that helps explain why Knuckles (of all people) is in charge, and because neither the island nor the Master Emerald ever appear in cannon anymore. Just, why? What the heck did Knuckles do with the emerald in the game? Was he not concerned that Eggman would steal it? Like so many things, it was just ignored.**

 **On another note, sorry if this chapter seemed a little dry/lacking in action, but I had to flush out this backstory, and get the first bits of the resistance in place.**

 **Next chapter will have much more action. And _edge_. **

**As always, reviews/opinions/suggestions are welcome, and I'll be back with the next chapter soon.**


	6. Army of One

**Author's Note:**

 **Again, I want to thank my reviewers and followers for the incredible amount of support this story has received.**

 **Awdures \- Thank you! I'm glad it made sense and was enjoyable to you. I hope you like the rest of the story just as much. **

**MobiusHero \- I'm happy you approved of it. And you're right, it really didn't make sense in Forces to have Sonic face a greater threat than ever before, and yet completely ignore the Chaos Emeralds. I get that SEGA has faced criticism for making almost every game plot rely on those things, but come on. Leaving them out of Forces completely was a mistake. A mistake that isn't repeated here. Anyway, regarding Silver. The Sonic cannon is a tangled mess. Silver has the most tangled story of all. 06 wiped its entire story away at the end, so the Silver from that game doesn't even exist anymore. And to be honest, I'm not taking the Rivals games as cannon here. The plots in those games were messy too, and it just doesn't make sense for the same Silver to come back from multiple futures. Each time the future is fixed, Silver's backstory and the way he grew up would change. It would be a different Silver coming back every time. And Generations... It doesn't even make sense that Silver or Crisis City were in that game at all considering 06 never happened. So basically, Silver's cannon is so messed up that I'm just giving him a clean slate here. That's the only way I see for this to truly make sense.**

 **NetRaptor \- Thanks for the support! Knuckles is an interesting character to write for this story, for exactly the reason you mentioned. He goes from lonely hermit to leader of the entire resistance, and we've only just started exploring that process. It's going to be fun. And on the note of Sonic's torture... The Phantom Ruby could do some sick and twisted stuff to Sonic if I really wanted to make this fic require a mature rating. Poor Sonic is gonna go through hell already as it is, and it's gonna be interesting to see the effects on his character afterward. Stay tuned!**

 **And on that note, here is the next chapter. More edgy and action packed than the last couple, so beware!**

* * *

Chapter 5 - Army of One

* * *

The air was heavy and silent over the Mobian hill country, as the sun beat down harshly from above. No sound was to be heard. Animal life refused to stray out into the oppressive heat, and no wind blew across the grassy hills. All was still and lifeless, except for the lone dark figure that lay sprawled out on one of the hillsides, with a single green Chaos Emerald laying inches from his limp gloved hand. His shallow breathing was the only sign of life for miles around.

Crimson eyes opened abruptly, and the figure gasped as consciousness made its return. Rolling over onto his hands and knees, the black and red hedgehog breathed heavily as he tried to remember what had happened. He knew he had been in some sort of fight before he blacked out, and adrenaline had shot through him upon awakening once more, not knowing if he was in a safe position. His head throbbed with pain, his thoughts were mixed and fragmented, and _chaos_ did he hate it when he couldn't remember. Glancing around quickly, he relaxed somewhat when he saw nothing but the desolate and lonely landscape, devoid of threats or company of any kind. He closed his eyes and took a deep breath, and slowly, his jumbled thoughts and memories coalesced into a more coherent picture as everything came back to him.

 _The mission. The Doctor's secret base and his massive arsenal. Omega in trouble. A masked jackal. Illusions and confusion and So. Much. Noise._

Shadow the Hedgehog shook his throbbing head, growling in anger. Infinite and the Doctor would _pay_ for this. He was the Ultimate Lifeform, and he would not be trifled with so easily. Picking his emerald up from the ground, he reached for his communicator to update Rouge. The little machine did nothing but spark and fizzle. Growling again, Shadow ripped the device off and threw it to the ground. _Worthless piece of scrap._

Looking around once more, Shadow saw nothing but the rolling hills. Eggman's facility was nowhere in sight, and Shadow didn't even know where he was. He looked up at the sun, beating down from high in the sky above. It appeared to be sometime early in the afternoon already. How long had he been unconscious? A day? A week?

 _Another 50 years?_ He thought wryly, shaking his head.

Where were Infinite and the Doctor now? What were they planning and when would they make their move?

Standing here would get him nowhere. Omega was probably lying in a ruined heap somewhere nearby, and Rouge needed to be told what the hell was going on. He activated his hover-skates and rocketed off, intent on finding his robotic ally - or whatever was left of him.

* * *

After half an hour of searching the surrounding hills at supersonic speeds, with the hot afternoon sun blazing down on him, Shadow finally found the shattered body of the robot. The dark hedgehog was not an outgoing or friendly individual by any stretch of the imagination, but his allies on Team Dark were the closest things to "friends" he would probably ever have. Seeing Omega like this, even though he was a robot and could most likely be repaired, filled Shadow with a burning rage. He had felt anger over the injury of his allies before, but it was never this bad. That jackal had utterly defeated OMEGA, and then had outright taunted and played with Shadow. _That_ would not stand. The Ultimate Lifeform hadn't felt a rage this strong since... Well... He'd rather not remind himself of that. He pushed the rage down and stored it away, promising himself to use later when he met Infinite again.

Gathering Omega's scattered parts together, he pulled out his emerald and warped back to Westopolis, where the team's headquarters were and where Rouge had been directing the mission from. Of course, fate decided that Shadow hadn't been through enough already, and decided to throw him another curveball. As the glow of chaos control faded, Shadow was left standing in Team Dark's HQ - only the HQ wasn't there.

"What. The. Hell."

He stood in a heap of shouldering ruins, with the rubble of collapsed buildings surrounding him on every side. Dust and ash were so thick that he couldn't see more than a few dozen feet in any direction. Eggpawns patrolled the flaming wreckage, and the thundering of giant metal footsteps betrayed the presence of giant mechs nearby. Smoke hung heavy and oppressive in the air, and if Shadow was any regular being, he probably wouldn't be able to breath.

It didn't make sense. He had just been here the morning before his mission to the Doctor's secret facility, where he had faced that masked jackal. _I must have been out of it for at least a couple days._ He realized. _Perhaps the confrontation with Infinite took a heavier toll on my mind than previously assumed._ That was a disturbing thought for the Ultimate Lifeform.

A multitude of questions now flitted through his mind as he stood amid the war-zone, with Omega's shattered form lying at his feet. _What in chaos name happened here? Is Rouge alright? Where was Sonic? Isn't he supposed to be watching out for and preventing this kind of mess? Was this the work of Infinite?_

He looked down again at the ruins he was standing on. This was all that remained of Team Dark's base, the closest thing to a home he had. And now it was gone. The city was decimated, his home was a pile of rubble, Omega lay in pieces at his feet, Rouge was MIA, and Shadow was royally pissed off. His left ear twitched at the sound of a blaster charging up, as a nearby eggpawn finally noticed him and took aim at him. Within an instant Shadow was standing above its shattered remains, fists clenched and eyes narrowed. That familiar rage was building in him again, and this time he wasn't going to fight it. He had made a promise to protect the planet, and yet here lay an entire city that had decimated by Eggman. Well, if he was too late to defend the city, he would by all means avenge it's fall.

There were obviously no innocent civilians left around. No surviving infrastructure to speak of. Nothing stood except Shadow and the soulless robotic minions that had caused this mess. Quelling anger or showing mercy was not something to worry about here. The Ultimate Lifeform stood alone amid the dark machinations of a madman, and let his rising rage flow through him. He tucked his chaos emerald firmly into his quills, closing his eyes and feeling its power radiate through him. Chaos was his element, and destruction was his calling. He would not hold anything back.

Crimson eyes opened, shining with the fury of a thousand suns. Chaos energy crackled in open palms, and teeth were bared in a feral growl. Hover-skates activated, and Shadow charged at the nearest group of robots, ripping through them like paper. He moved on instinct and adrenaline and _rage_. Pure, unadulterated, rage. The next squad of eggpawns didn't see him coming until the first one exploded, and the rest had barely raised their weapons before they were lying in pieces among the rubble. Shadow was nothing but a dark blur racing across the ash covered wasteland, lit only by the flickering flames in ruins around him, and obliterating everything in his path. A savage fist shattered a robotic skull, a merciless kick sent another into a wall. A chaos spear shot through three at once, and an animalistic growl escaped his throat he ripped the arms off another one. A heavy thud shook the ground, announcing the presence of a giant mech, and Shadow launched himself into the air. Narrowly dodging a spiked metal fist, he charged at the robot, curling into a powerful spin-dash and shooting straight through its heart. Another heavy thud sounded as the metal corpse collapsed, and the Ultimate Lifeform shot off to continue his offensive.

Darting like a phantom through the smoke and ash, weaving through ruined buildings and large pieces of rubble, he ripped through his enemies at blazing speed. He was a living weapon, deadly and precise in his movements, vicious and unforgiving in his assault. Woe to anything that stood in his way. Eggpawns dropped like flies before him, and hardly a blaster was raised at him before its owner was destroyed. He had just ripped the head off of one, and was about to charge off in search of more, when he was interrupted by a dark and sinister voice.

"What a pleasant surprise."

Eyes blazing like the fires surrounding him, Shadow turned quick as lighting to face the source of the familiarly distorted voice.

Hovering like a glowing specter amid the smoke above the wreckage, Infinite starred down at the raging hedgehog. He had one arm crossed over his chest and the other resting on top of it, reaching up to touch the front of his mask with two fingers.

"Infinite." Growled Shadow, eyes narrowed and fists clenched.

"We meet again, my dear Shadow. It appears I've touched a nerve with the razing of this city."

The Ultimate Lifeform snarled in response and launched a chaos spear at the jackal, who hovered impassively as it passed straight through him.

The masked villain slowly shook his head. "Oh Shadow, still so much to learn."

The hedgehog's face contorted again in rage, and he launched himself at Infinite with a blinding fury. Infinite blinked out of existence as Shadow was about to hit him, reappearing a split second later as he drove a fist into the hedgehog's gut.

Shadow landed hard on the ground, grunting at the impact. He scowled up at Infinite, then quickly teleported above him, but the fist he sent toward the jackal's head once again passed through as if through thin air. And once again, Shadow found himself on the ground after a savage kick from his seemingly invincible foe.

"What a shame. I thought you'd have more fight in you than this." Infinite taunted from above as Shadow stood up again.

"How... how are you doing this?" The bruised hedgehog questioned, feeling completely at a loss to explain the power of his enemy.

The jackal shook his head. "Ahhh. This must be the part where you expect me stand here and explain the secrets my power." The tone of his voice was beyond sinister. "I have a better idea."

As he finished speaking, somebody sent a kick flying towards Shadow's head from behind, and the hedgehog barely ducked out of the way in time, rolling to the side and halting in a crouch to assess this new enemy now standing in front of him.

It was himself.

If Shadow had been standing, he almost would have thought he was looking into a mirror. But this was no mere reflection. A perfect replica stood before him, staring him down with hatred burning in its crimson eyes, and fists clenched at its sides.

Shadow stared incredulously at the replica, unsure of whether to feel more confused, pissed off, or oddly flattered. This wasn't the first time he had come across a replica of himself, but even the infamous Shadow Androids didn't come close to looking as real as this. The way the quilltips blew lightly in the smoky wind, or the rise and fall of the chest as it breathed... it looked so _real_.

Infinite's laughter as he stared was just as disturbing as Shadow remembered it to be.

"Impressive, isn't it Shadow?" The jackal gloated from behind his mask.

With that, the replica snarled and charged at him, and Shadow barely dodged out of the way. He teleported behind the imposter and charged at it, aiming a kick at its head. The double ducked and spun around to face him.

 _Very impressive._ Thought Shadow silently, who had been carefully watching how fast the double reacted. He deflected the fist sent towards his face, and dodged to the side of the next one. _This thing is just as fast as I am. But I have one thing it does not._ He smirked, reaching for and feeling the power of the chaos emerald in his quills flow through him.

"Chaos Control!"

The familiar glow of chaos power surrounded him, and time slowed to a crawl. He ran behind the double, kicking it into the air, before quickly teleporting up and slamming it back down to the ground, where it landed with a sickening thud. Time resumed its normal flow and Shadow landed in a crouch above the bruised and bleeding form of the replica. _Bruised and bleeding? Just how real was it?!_

He turned to glare up at Infinite, who had been watching the fight with muted interest. "What was that?" He demanded angrily.

"Oh Shadow." The jackal taunted. "Is your memory so fragile that you don't recognize when you see yourself?"

The hedgehog narrowed his eyes, growling in anger. "I'm done here." He said darkly. With another shout of "Chaos Control!" Shadow paused time and leapt up toward Infinite, intent on ending this once and for all. But the punch he aimed passed right through the Jackal, and he landed back on the ground. Time resumed and Infinite's form flickered out of existence. The defeated replica also vanished without a trace. The wind picked up, and the smoke around Shadow suddenly thickened immensely. "Poor foolish hedgehog." Infinite's distorted and malignant voice sounded from the blackness in front of him. "You can't beat me. You are weak!"

Shadow coughed as he inhaled the thick smoke, his eyes stinging as forced them to stay open, watching the masked villain reappear in front of him, with fists clenched and with the ruby colored stone on his chest glowing brightly through the dark smoke.

"It's... not possible.." Shadow coughed out as the smoke tore at his lungs. "None of this is possible!"

Infinite laughed then, and the loud, harsh sound of it seemed to come from everywhere at once. "Shadow, you have no _idea_ what's possible."

A burst of red light emanated from the stone on the jackal's chest, and Shadow was suddenly back in the clear air of the hill country, staring at Omega's shattered form. A second later he was watching a robotic army rampage through Westopolis. Another flash and he saw Rouge coming under fire as she tried to flee. Then he saw her lying on the rubble-strewn street, pale and lifeless. Next he saw Sonic, lying bruised and bloody in a cell. Tails trembling and fleeing the burning city with tears in his eyes. Omega's pieces rusting in a corner. Rouge lying dead again, but this time in some sort of jungle. More cities destroyed. Himself in the mirror looking like death. Rouge alive, but imprisoned and tortured. Sonic lying dead on a volcanic slope. The Doctor sitting enthroned in a palace. Inhabitants of the world forced to work as slaves. Tombstones for his allies and comrades as he himself was forced to live on, agelessly watching everything else die around him.

These images and more tore through his mind as Shadow cried out in pain, collapsing to his knees and clutching his head. "No!" He yelled out through the storm of horrors around him. "Stop this!" He tried running, but he couldn't escape the images. He clamped his eyes shut but still they were there. Infinite's laugh echoed through his mind, and his head felt like it was about to explode. Desperation clawed at his mind, and Shadow reached back to rip the Chaos Emerald from his quills.

Crimson energy flared from within him as he channeled the emerald's power through his body, charging it and then expelling it in every direction in a desperate effort to end the assault on his mind.

" _Chaos Blast!"_

The scenes flashing around him suddenly shattered, and he found himself back again laying amid the rubble of Westopolis, with the smoke no longer thick enough to choke him. Infinite was nowhere to be seen, but he might return at any moment.

Head still throbbing, Shadow gripped the emerald tightly in his hand and called upon its power one more time.

"Chaos Control."

And in a flash of light, he was gone.

* * *

He reappeared an instant later in the plains beyond the outskirts of the city, where the air was blessedly fresh and free of smoke, and the sun shown brightly from low above the ocean horizon to the west. Breathing heavily, Shadow tucked the emerald back into his quills, and scanned the landscape around him.

To his west the plains continued for only a few miles, steadily dropping lower until they ran into the ocean. To his north were the smoldering ruins of Westopolis, covered by a thick black cloud of smoke. To his east the plains continued for a few dozen miles, before rising into the foothills of the distant Greyback mountain range, which ran for hundreds of miles north and south along this western coast. Off to the south, the plains between the hills and the sea stretched out for miles and miles, but their uniform appearance was broken by a dark mass moving slowly across them.

 _Refugees from the city._ Shadow realized. _They are probably in bad shape, with a long walk ahead of them to any sizable town._ Sighing, he activated his hoverskates, racing off to offer what help he could. He didn't like to deal with crowds of people, let alone crowds of panicked and hurt people, but he wasn't heartless enough to just ignore them after a tragedy like this. _Besides,_ he thought, _maybe Rouge is with them. She doesn't usually follow a crowd, but I don't have a better idea of where she could be._

His thoughts turned briefly back toward Omega, whose broken body was still left behind in the ruins of Westopolis. _I'm sorry Omega._ He reflected grimly. _There's nothing I can do for you right now._

As he approached the throng of refugees, a chorus of horrified screams rose up to greet him, ripping him from his thoughts. The citizens were staring and pointing at him with terror _What now?_ He groaned mentally.

As he moved closer, he heard with more clarity what the fleeing crowd was screaming. "It's him!" "Run!" "Its Shadow!" "He killed Sonic!" "Run for your lives!"

"What the hell?" Shadow asked aloud as people fled from him in all directions. _I am_ so _not in the mood for this right now._

Deciding that politeness was getting him nowhere, the striped hedgehog darted forward and grabbed one of the fleeing citizens, a young male bird, holding him tight so he couldn't flee like the rest.

"I'm not going to hurt you!" He shouted over the bird's terrified screams.

"You're lying!" The bird cried. "We saw you helping Eggman! You killed Sonic!"

"I didn't... Eggman... Sonic is _dead?!_ "

His grip on his captive slackened, and the terrified bird twisted away and fled. Shadow let him go, his stomach dropping as the pieces fell into place.

 _The Doctor and Infinite attacked Westopolis. They used a replica of me_ _to attack, and now everybody thinks I'm working for the Doctor again. Sonic must have tried to stop them, but he couldn't stand a chance against Infinite's power. Against those illusions. Against that fake_ me.

Shadow gritted his teeth, watching the fleeing crowd move farther and farther away from him. _Damn you Eggman. Damn you for using me like that, and turning the world against me._

His seething was interrupted by the drone of a large swarm of buzz-bombers approaching from the north. _Apparently Infinite realized I got away._ He thought wryly. Then he turned to glance in the direction of the throng that had just fled from him. _Or they're after the refugees._

With a sigh, Shadow activated his hoverskates and charged toward the swarm. Even if that crowd hated him, he was still bound to protect them. At the very least, he could distract the swarm with a more important target.

A few chaos spears caught their attention quite handily, and soon Shadow was racing over the plains at high speed, leading the swarm away from the refugees as he dodged the laser blasts raining down on him from above. _The things I do for people who hate me._

Jumping into the air, Shadow curled into a ball and rocketed toward one of the robots, cutting through it and then shooting off towards the next one. Bouncing from enemy to enemy, smashing and cutting through them, working his way through dozens of the flying robots. Within a few minutes, he had destroyed a sizeable chunk of the swarm, and the rest retreated back towards Westopolis. Shadow landed in a crouch back on the ground, deciding to let them go.

 _What now?_ The hedgehog wondered, looking out to the west again, watching as the sun crept ever lower to the horizon. _It's getting late._

"I can't stay here." He muttered, shaking his head and reaching for his Chaos Emerald.

 _Team Dark is gone, all of Westopolis is gone, GUN has likely branded me a traitor and a terrorist by now. That doesn't leave me many good options._

His gaze turned upwards, and he shifted the emerald back and forth in his hands.

 _I don't particularly want to go back. But right now it might be the only safe place for me to lay low and recover while I try to sort this all out._

Letting out an exhausted sigh, Shadow looked down into his emerald, and murmured "Chaos Control."

* * *

An instant later, he stood on a cold metal floor, breathing in the stale and motionless air, looking out a wide window down at the planet he had just left behind.

 _Back here again._ Shadow thought with a frown.

He turned away from the window and shook his head in an effort to keep the memories at bay. Igniting his skates, he navigated rapidly down halls he had memorized decades ago.

Reaching a large room containing the station's power core, he took out his emerald and slotted it inside. Lights flickered on, air began to circulate, and a low hum filled the empty halls as Space Colony ARK came alive once more. Nodding once in satisfaction, Shadow left the room and returned to the viewport. Sitting down and staring at the planet below, he silently contemplated his situation.

Infinite was obviously a much greater threat than he had anticipated. The mysterious power wielded by the masked jackal seemed to be... well... infinite. At any rate, returning to Westopolis or seeking out another conflict with the villain would virtually be suicide unless he discovered an exploitable weakness. Trying to discover such a weakness, if it existed, would be a lot easier if his teammates were still with him.

 _But Omega is lying in a broken heap down there in the ruins of Team Dark's HQ._ _Rouge could be anywhere... or dead._

Shadow felt guilt tug unpleasantly at his heart as he thought of his teammates. He had been too late to save Omega, and now he couldn't even risk going back to Westopolis to retrieve the body. As much as he hated to admit it to himself, Shadow knew he was no match for Infinite right now. And Rouge... Shadow was more worried for Rouge than he would like to admit. She was the closest thing he had to a friend, and she was his most loyal ally. It was very disturbing to him, not knowing her fate.

The fate of Sonic was less of a mystery, but almost just as disturbing to think about. Despite the tense rivalry between them, Shadow had always viewed Sonic with a certain measure of respect. The blue blur was an idiot, in Shadow's view, but he was a good-hearted and amazingly skilled idiot. Sonic was always there when you needed him, never giving up when it really mattered, forever looking forward to the next adventure. And no matter what he faced, no matter the pounding he took, no matter the odds, the blue blur always seemed to pull through it. For Sonic to die like this, perhaps at the hands of a false Shadow... it just seemed so _wrong_. And if it seemed wrong to Shadow, of all people, how were Sonic's friends taking all of this?

 _Are Sonic's friends even still alive? I suppose it doesn't matter. If they are, they certainly won't accept any help from me. On that note, neither will GUN. I am alone, and the entire world has become my enemy._

"Hmph. So be it then." Shadow said resolutely as he stood up, crimson orbs blazing as he looked defiantly down at the world below. His mouth was set in a grim line, and his fists were clenched tightly at his sides. "I will fight alone, even if the whole world stands against me, and I will remind them _all_ just what kind of a being they have made an enemy of."

If the world was to burn, here was one hedgehog ready to charge into the flames. How it would end, he didn't even care to try guessing. But one thing at least was sure.

Shadow the Hedgehog would continue the fight until his very last breath.

* * *

 ** _"If the world chooses to become my enemy, I will fight like I always have!"_**

 ** _Author's note: Alright, this is the first glimpse we get into what Shadow was doing for the six bloody months that the game just ignored. I hope I didn't write him very out of character, as I think Shadow is one of the most complex figures in this story. I wanted to explore his thoughts a bit through all of this, and show some of his softer side reacting to the death/disappearance of his teammates, while maintaining the edgy nature he is famous for._**

 ** _Anyway, Shadow actually has a pretty good reason for staying away from the resistance all those months. He naturally would be branded an enemy by the free world, and attacked the moment he was sighted. Plus, his nature is such that he usually prefers working alone anyway. I brought the ARK back because Shadow needed somewhere to hide from both sides, and the ARK is still just sitting out in space unused and abandoned. It's a familiar place that Shadow knows well, and has simply been ignored for years, so why not?_**

 ** _Also, GUN is another plot hole in the official plot for Forces. Last we saw, Shadow was working as an agent for them. But the Forces comic and game story leave GUN out of the picture completely,_** ** _and seem to imply that Team Dark operates on its own. Soooo... Even though Team Dark/Shadow operate without supervision in this story, I decided to include GUN here nonetheless, since they are a very real military force in the world, and there's not any good reason why they wouldn't still be around._**

 ** _But moving on, I hope to have the next chapter up this weekend, and move this story along. We've still barely gotten started here, and it's only going to get more fun going forward._**

 ** _As always, reviews/suggestions/opinions are welcome, and I'll see you folks in next update._**


	7. Captive

**Sorry for the big delay, folks. Things got crazy over the past month and a half, and I couldn't find the time to really sit down and write. But I want you all to know, I did not and I will not ever let this story go, and now that I'm more free again, you can expect more chapters much sooner!**

 **As always, thank you to those who reviewed, and sorry again for the wait.**

 **Awdures \- Glad you liked it. The dynamic between Shadow and infinite is an interesting one, and you'll see a lot more of it further on in the story.**

 **Brisk Afternoon** **\- You're quite welcome. Shadow it going to have a unique role to play here, even on his own.**

 **NetRaptor \- Yeah, the game left a lot of things out for the sake of simplicity, lol. But they won't be left out here. **

**Mitha Sentro \- Infinite had so much potential, but SEGA just ruined it. He could have been the greatest villain in a long time if they took him seriously. Anyway, I'm glad you're enjoying the story!**

 **MobiusHero \- Just because the villains are fake, doesn't mean they can't be fun. The story just has to take them seriously, unlike the game, lol. You'll see a bit of that in this chapter. And I'm glad you're satisifed with Shadow's story thus far. We're going to see plenty of Shadow's dark side, even though he's technically not evil here. His arc in this story is my favorite, and we've barely gotten into it. **

**The Dragon Legend \- Great minds think alike? Lol. It is a good spot, and it's the only one that really allows us to explain what happened to the master emerald through all of this. I'll have to check out your version at some point. I'm glad you're enjoying this one so far.**

 **Ways \- I actually realized that fact about the resistance HQ a week or so after a wrote that chapter, lol. I just figured that Angel island still works better and the HQ location never actually mattered much in the game story anyway. And yeah, canon for Sonic games is all kinds of messed up. So I'm kinda just taking whatever works best, and since GUN is usually involved wherever Shadow is, I decided to bring them in here. Besides, they'll be an important factor later in the story. **

**And with that, here is the next chapter...**

* * *

Chapter 6 - Captive

* * *

Unconsciousness was reluctant to give up its hold, but ever so gradually it gave way to a rising tide of awareness that flooded through Sonic's bruised and battered body. Emerald eyes opened sluggishly, staring blankly at the metallic ceiling above them, and stiff fingers flexed slowly within dirty gloves. His mind was foggy and concussed, and for a few moments, his only coherent thought was how much his head hurt. He shut his eyes again, gritting his teeth at the throbbing within his skull, and tried to sit up against the protests of his bruised and aching body. After almost blacking out again at the effort, he finally managed it, and found himself facing nothing but a metal wall. Slowly, and with some difficulty, he turned his head to look around, and felt his neck crack in the process.

"Ouch." He mumbled out, reaching up to rub the back of his neck. _I'm pretty_ _stiff here... How long I've been out of it? And where_ _... Where am I?_ _Some sort of cell?_ The hero questioned, through the haze of pain clouding his mind. A glance down at his legs revealed a pair of high-tech cuffs around his ankles, and though his hands were free, a quick attempt to fiddle with the restraints was rapidly rewarded by a violent electric shock that discouraged further tampering.

 _Well, this is something you don't see everyday. Sonic the hedgehog, captured and restrained. You'd think Eggman could at least offer me a bigger room, wherever it is he's keeping me._

The cell he occupied was small - _far_ too small for his liking - and bare of any kind of furniture. It was bounded on three sides by solid metal walls, and the remaining side was open, but blocked by a force-field of some kind. It separated the brightly lit room from a dim hallway on the other side. Several security cameras watched him from just behind the force-field, and he couldnt resist briefly sticking his tongue out at them before turning his mind back to the predicament at hand.

 _So, I'm captured. It's not like I haven't been imprisoned before, I'll get out soon enough. But what happened to me? It feels_ _like I was run over by a tank! The last thing I remember is Tails calling for help..._

Suddenly, in the midst of his ruminations, the pain in Sonic's head intensified as the memories came rushing back. He cradled his throbbing head in his hands as he recalled Westopolos burning, Eggman's new robotic army, the return of villains from his past, and the strange and powerful newcomer who had tossed him around like a rag doll. Groaning aloud, he grit his teeth and waited for the pain to subside.

 _I was beaten._ The hero realized with a shudder. _They had me. That masked creep could have killed me if he wanted._ Then a more potentially terrible realization set in, and Sonic nearly stopped breathing at the thought of it. _What happened to Tails?_ The last Sonic had seen of his little brother, the kit was picking himself up off the ground after Shadow had kicked him into a pole, which didn't exactly inspire a lot of hope that Tails had gotten away safely. _I'll never forgive myself if he didn't make it out okay. And I'll never forgive Shadow either._

The thought of the Ultimate Lifeform turned Sonic's mood even more sour, as he felt the painful sting of betrayal stab at his heart. While he and Shadow had never exactly been on friendly terms, the blue hedgehog had always felt that the Ultimate Lifeform was a hero at heart, even if he wasn't the nicest guy out there. Shadow, it had seemed, respected him enough to leave him be and even help out in fighting Eggman from time to time. And yet, Shadow had stood with the Doctor as Westopolis was attacked and its citizens murdered or forced to flee. _What happened to his promise to Maria? Does he not even care about the lives he's ruining? Doesn't he feel anything?!_ It seemed as if Shadow had completely rejected any conscience he might have once had. The image of the black and red hedgehog's feral grin as he savagely attacked Tails was seared into Sonic's mind, a painful reminder of the betrayal, and a knot formed in his stomach as he continued to worry over the kit's fate.

His worries were interrupted, however, by the sound of footsteps in the hall outside his cell. Sharply pointed silver and black boots clanged against the metal floor of the hall with every step their owner took, and Sonic clenched his fists as he stood up to face his foe, ignoring the continued pain in his head.

The masked stranger regarded the hedgehog silently through the force-field, head tilted slightly to the side, arms crossed over his chest. The hero stood with fists clenched at his sides, staring back unflinchingly for a moment, then dropped into a relaxed stance and casually rubbed his nose with one finger.

"So you're Eggy's new toy, huh? What makes you so interesting to him, I wonder?"

The stranger's only reply was continued silence.

"I have to admit I'm impressed. It's not easy for somebody to take me on, but you did, and now here I am in this cell." Sonic narrowed his eyes before continuing: "So who are you, and just what is it that makes you so powerful? Is it something Eggman did to you?"

Finally, the masked being spoke, in a demonically distorted voice. "You're not even worth my time. For so many years, Eggman has tried to defeat you. But for all your arrogance and wit, you are nothing more than an insect waiting to be crushed underfoot. If it were up to me, you'd already be dead."

Sonic grinned at the response. "I'm not worth your time, but yet here you are. Somehow I don't think-"

He never finished that sentence, cut off by a powerful kick to his back that sent him sprawling forward into the force-field between him and the stranger. He hissed at the sting for a moment, before the field blinked out of existence and he collapsed out into the hall. A kick to his side forced him to roll over, and Sonic found himself staring up glaring crimson orbs.

"Shadow." the hero greeted with barely disguised hostility.

The black hedgehog made no reply, simply looking over to the masked one, who gave a slight nod and began walking down the hall. Shadow then forcibly grabbed Sonic's wrist, and followed the dark stranger down the hall, roughly dragging the hero behind.

"I appreciate the help Shadow, but I could walk perfectly fine if you took these cuffs off my legs." Sonic protested with biting sarcasm. "Maybe we could even have a little race. For old times sake?"

The Ultimate Lifeform made no reply.

"What's the matter? Afraid you'd lose, _faker_?"

Still no answer, and Sonic was getting fed up at this point. He was about verbally lash out again, when they reached a door at the end of the hall. The masked one stepped aside as it opened, and Shadow yanked violently on the arm of his prisoner, dragging him through the door and tossing him into the middle of a large, dark room.

Jade eyes shot an angry glare at the striped hedgehog, before turning to gaze at the only prior occupant of the room.

"Enjoying your stay, Sonic?" The rotund figure grinned victoriously from the shadows, hands clasped behind his back.

Sonic raised an eyebrow. "It's a nice place you've got here, Egghead. But the room service needs a little improvement."

"Ah, well, I'll see what I can do to make you more... comfortable." The doctor finished, sarcasm dripping from his tone. "After all, I do plan on keeping you here for quite a while."

"Aww, do you enjoy my company?"

"Of course I do, rodent, or you would not still be alive."

"How touching." Sonic responded flatly, eyes darting across the room, straining to see in the darkness.

"I brought you here, because we've known each other for so long, and I have something to show you. Something important that we need to see together. The culmination of our long relationship."

Sonic sighed, and turned a tired gaze on the shadowed form of the doctor in front of him. "As much as I enjoy your heartfelt speeches, Eggy, do you think we could get on with it already?"

Eggman paused for a moment, before responding. "If you insist." And if Sonic didn't know better, he'd think the mad scientist sounded a bit sullen.

The doctor pressed a button at his wrist, and Sonic squinted as electric light flooded the formerly dark room, illuminating the red jacketed villain and his blue spiked prisoner. The room was larger than Sonic's cell, but not by much. On one wall was mounted a large screen, filled at the moment with the sinister black and red logo found plastered on every piece of Eggman technology. The other walls were completely bare, save for the security cameras in their upper corners.

"I've kept you sedated while I moved you here, you know." Spoke the evil mastermind. "It's been more than a week since I defeated you. And everybody belives that you're dead."

The hero raised an eyebrow. "Just me?"

The doctor cackled. "Oh don't worry. Your little fox friend is still alive - for now. He ran away, believing you to be dead, and nobody has seen hide nor tail of him since."

Sonic couldn't help but breath a sigh of relief.

"But I'm afraid that's the only good news you'll get from here on out, my little nemesis. Sooner or later, my armies will find him. You know they will. And with you gone, he won't have the spirit to stand up and fight against me."

The blue hedgehog awkwardly maneuvered his restrained legs in order to stand up, and then looked to the villain with a smile. "He'll never give up, Eggman. Never."

"Hmmmm. Perhaps not. But the rest of the planet has." Rejoined the doctor, pressing another button on his wrist. The TV screen on the wall flickered, then displayed a dreadful scene. From high in the air came a panoramic view of Westopolis - or what used to be Westopolis, anyway. The city lay in ruins, pockmarked with craters and covered in debris, overshadowed by a cloud of dust and ash that hung above the city and stretched far out to the sea. Then the view changed to a feed from downtown Station Square. This city was perfectly intact, but throngs of its citizens crowded in the streets, dressed all in black with their heads bowed down as they mourned the fate of the planet and its hero.

"You were their protector, you provided hope to these people, Sonic. But you failed them, and now they take to the streets in mourning, because they know their pathetic lives are almost over."

Said protector stared transfixed with mounting horror at the images on the screen. A view from a tower in Metropolis was now being shown, looking down to citizens on the ground who were scrambling to and fro in abject terror, hurriedly trying to evacuate the city. Then the camera panned up to display a massive army of robots on the horizon, marching steadily and unopposed toward the helpless city. Sonic clenched his fists and muttered: "You're sick, Eggman."

The doctor shrugged, reaching over to turn the screen off. "And you're shortsighted. The world will be a far better place when I'm done with it. You'll see."

The blue hedgehog growled, and despite the restraints on his legs, tried to awkwardly lunge at Eggman. Shadow was instantly in the way, delivering a vicious punch to the hero's jaw. As Sonic collapsed to the floor, the masked stranger, who had been watching in still silence up till now, raised an open hand toward him. The glowing gem mounted on the jackal's chest flared in brightness, and at that instant, the hero's mind erupted in pain. He curled helplessly into a fetal position with his hands on the sides of his head, yelling in pain under the mental assault.

"That's enough." The doctor commanded, and the masked one acquiesced. Sonic released his throbbing head as the pain subsided, breathing heavily as he turned to stare at the black and silver figure.

Eggman sighed. "You're going to be staying here for a long time, Sonic. I'm going to make you watch, as my empire rises from the ashes of this world. Only then will my triumph be complete. You would be far better off if you'd learn to just be a good little prisoner." Then the mad scientist pressed another button at his wrist, and a portion of the floor slide aside to reveal a pool of water beneath. The blue hedgehog froze at the sight of the liquid, as the villain continued his malicious monologue: "And while you're here, I think it's long past time I take my revenge for all the defeats you've handed me over the years."

With that, he nodded toward Shadow, who forcibly grabbed Sonic by the neck and began hauling the struggling hedgehog to the water's edge. Bruised, tired, and restrained as he was, the panicked blue hedgehog was powerless to resist. He could do nothing more than take a quick deep breath, before his head was forced underwater.

* * *

It was several hours later, before the door to the room opened again, and Shadow hauled Sonic's limp and wet body back out into the hall. The hero coughed hoarsely, still trying to expel the hateful water in his lungs.

"You're weak." Rebuked the Ultimate Lifeform, as he tightened his already bruising grip on the blue hero's wrist.

Sonic coughed again, before responding bitterly "Yeah, well, I'd like to see you get kicked around, sedated for a week, and then... * _cough_ * tortured all day." After another coughing fit, he continued: "What's the matter with you anyway? Why are you working for Eggman?"

"I do what I please." Growled Shadow as they reached Sonic's cell.

"Even if Maria would despise you for it?"

The next instant, Sonic was pressed against his cell wall with a gloved hand wrapped tightly around his throat.

"You. Don't. Get. To talk. About. Her."

Sonic struggled in vain against the hand at his throat, too weak from captivity, torture, and lack of food. "You.. defile... her... memory..." he coughed out.

Shadow snarled and flung him to the floor, before delivering a powerful kick to his gut. "Stay down." He warned. "And don't you dare speak of her again."

The hero coughed violently, and lay exhausted on the cold metal floor of his cell. He didn't have the strength or energy to fight anymore. He said nothing, only watching with simmering anger as Shadow activated the force-field and walked away.

* * *

From another room, filled with TV screens displaying security camera feeds, Eggman watched the scene play out with great interest. "Excellent work." He told the masked figure at his side. "If I didn't know better, even I would think that was the real Shadow."

The jackal nodded in acknowledgment, before asking: "What of Sonic? Do you truly intend to keep him alive?"

"Of course." The doctor responded, stroking his mustache. "Sonic has been a thorn in my side for years now, and it's only right that he be forced to see the magnitude of his failure and my final triumph." He cackled sadistically. "I'm going to make him suffer. And eventually, I'm going to break him."

If the masked one had any response to that, he wisely kept it to himself, instead turning to look thoughtfully at the video feed of Sonic lying exhausted in his cell.

The hero was bruised and weak, mentally and physically worn out, but he was far from defeated. His mind was active as he lay on the hard cell floor.

 _One day._ He vowed to himself. One day he would escape, and he would make it all right. He didn't know how, but he knew that he had to. He would stop Eggman from winning, he would make Shadow pay for his betrayal, and he would save the world from its terrible fate. One way or another, he would do it, or he would die trying.

 _One day._

* * *

 **So, there's that chapter. This one, even though it's shorter than most, actually gave me a lot of trouble. I wasn't exactly sure how I wanted to do it for a while, but I wanted to make it right since it sets up some things much later on in the story.**

 **The biggest difficulty here is getting Sonic's character right. You don't often see him in a situation this serious, and adapting his usually laid-back and witty personality to this chapter was pretty tricky, so I hope it came across well. I wanted to explore Sonic's reaction to all this, things like not initially knowing what happened to Tails, or especially his interaction with "Shadow". Because even though this Shadow is a fake, Sonic doesn't know that. So this presents some interesting opportunities for me (via Eggman and Infinite) to mess with Sonic emotionally. Because even though Shadow and Sonic have never quite been on friendly terms, Shadow has technically been one of the good guys for quite a while, and I'm pretty sure Sonic would feel rather betrayed to see him working for Eggman like this.**

 **Additionally, it's the first time I write more than a couple sentences for Eggman, so I hope you find his character alright. I feel pretty good about how I wrote him, even though I take him a bit more seriously than SEGA does. It doesn't help that SEGA itself has changed his character several times over the series, but that's another discussion.**

 **Anyway, I hope you enjoyed that chapter, since it's the last we'll see of Sonic for a while. Please don't hesitate to leave a review with your opinions, suggestions, etc.**

 **Until next time!**


	8. Finding Friends

**Alright, here's the next chapter for you folks. I could have had it up a couple days ago, but the site has been having some problems with uploads lately, so hopefully that doesn't keep happening.**

 **Anyway, this chapter much less intense than the last couple, but it's important to set up some things going forward. As always,** **a big thank you to my wonderful reviewers - I'm continually surprised at how much support and love this story has received.**

 **Mitha Sentro \- Thanks for the encouragement! **

**NetRaptor \- I thought long and hard about just dealing with Sonic's torture in flashbacks, but I felt it was important to give more detailed account now, to help explain some things that happen later. **

**Infinite's Ruby \- I'm glad approve of it, and hopefully I don't keep you waiting too long. :)**

 **And without further ado...**

* * *

Chapter 7 - Finding Friends

* * *

Dawn was just beginning to break over the calm and wide western ocean. The monotonously dark sky ever so gently and slowly gave way to the golden glow of morning, heralding the soon rise of the sun. High above the still waters, floating serenely through the heavenly mists, Angel Island gently carried its precious cargo and its three solitary passengers.

Silver the hedgehog awoke from his slumber, just as the western skies were blooming into the golden and reddish hues of daybreak. Everything around him was calm, still, and quiet. The tranquil beauty of the environment was unlike anything he had experienced before. With a flex of his wrists, a cyan glow surrounded him and he floated into the air, off toward the eastern coast of the island. Perching himself on a rocky ledge, he stared in wonder as the radiant disk of the sun peeked over the horizon, unobscured by the polluted and scarred skies he was used to seeing in the future.

 _Everything is so beautiful in his time._ He reflected. _How could anybody let this amazing world decay into the one I was born in?_

Footsteps behind him pulled the hedgehog from his thoughts, and he turned to see Knuckles approaching calmly. The echidna sat down on the ledge next to Silver, and joined him in staring out at the dawn.

"How long have you been up?" He asked calmly.

"Not long." Replied Silver. "Just long enough to come out here and see the sun come up. This is only the second time I've really seen a sunrise, you know? In my time, the skies are always cloudy and polluted... I never knew how colorful it could be."

Knuckles was silent for a moment, before murmuring: "It really is something from up here, isn't it?"

"It sure is." The hedgehog voiced in agreement, before inquiring: "How's Tails doing?"

"He was still sleeping when I left him. Kid probably needs it." Knuckles answered with a shake of his head. "From all accounts he's had a pretty rough couple of days."

Silver nodded. "I know he did. He was an emotional wreck when I found him yesterday."

"I'm not surprised, with what happened to Sonic." The echidna muttered. "That hedgehog practically raised Tails, all on his own. And now... Who knows what happened to him."

Silver looked down, fiddling with his hands in his lap. "It doesn't bode well for us if Sonic is truly gone. You saw what that document said. You know what it means."

"I know." Knuckles answered, staring out at the horizon. "Believe me I know. But what choice do we have?" He turned to look at the hedgehog next to him. "We can't just sit here and do nothing. I did that in your timeline, and look how it ended up."

The future hedgehog nodded. "So what do we do instead? What can we do?"

"We'll do what we decided yesterday. We'll fight back however we can. But first things first, we need some backup. We three can't fight this war on our own. Let's head back to Tails, and we'll make our plans for the day."

* * *

The young fox awoke groggily at the sound of their footsteps, but after a quick drink of water and a few pieces of dried fruit, he had shaken most of his drowsiness off.

"I'm doing better." He said when Silver asked how he was feeling. "Still pretty sore in some places, but that's probably to be expected after a run in with Shadow like that." The kit shook his head, before adding forlornly: "I just wish Sonic were here."

"We all do Tails." The white hedgehog comforted. "And we'll do everything we can to rescue him, if he's still out there. I swear it."

"Let's not get ahead of ourselves though." Interjected Knuckles. "We already have a lot of work to do."

Tails nodded resignedly, while Silver patted him on the back. "So what's the plan, commander?"

The echidna raised an eyebrow at the title, before speaking: "We need allies. Friends to help us in the fight. We'll also need supplies, you can only get so much food from foraging on a floating island."

"It would also be good for us to all have communicators, and some tech support up here." Tails interjected. "We need to be organized. I could set up a lot of communication and security systems here, I just need the parts."

"Where do you plan on finding them?" Queried Knuckles.

"If I build it from scratch, it wouldn't be hard to find pieces at all. Broken down Eggman robots would probably be enough. It shouldn't be too hard find some, near and around Westopolis."

"Is that safe though?" Pondered Silver. "What if those villains are still down there?"

"If I see one of them, I'll just hightail it." Tails shrugged. "I'm fast enough to keep up with Sonic some of the time, I should be fast enough to run away if I need to."

"That works for me." Knuckles announced. "You can handle that, Tails, while Silver and I worry about finding some allies."

"Who do you have in mind?" Asked Silver.

"My first instinct would be to get the Chaotix." Knuckles replied. "They may not be the best fighters, but they've got spirit, and I can count on them to have my back."

Tails nodded in approval, but Silver was lost again. "Who?"

"They're friends of mine from way back." The echidna informed. "I helped them fight against Eggman when we first met, and I know they'll help us out now. Go to the Chaotix detective agency in Station Square, and ask for their help. Tell them that I'm the one asking for it."

"Detecive agency." Silver repeated in disbelief. "We're facing a robotic army and the potential end of the world as you know it, and your first instinct is to go find some detectives?"

"Yes, it is." Knuckles shot back with a glare. "And I'm in charge here, so you're going to do exactly what I say."

"Fine, fine." The hedgehog raised his hands placatingly. "Whatever you say boss. But why am I going instead of you, when you're the one they know?"

The echidna looked at him as if he had grown a second head. "I'm staying here with the emerald. It would be foolish to leave the island alone now."

"Oh."

"And while you're gone," Knuckles continued, "I'll forage whatever food I can here. We can figure out a long term solution for that later."

"While you're in Station Square," Tails broke in, "see if you can find Amy Rose. That's where she was staying, last I heard. We'll need all the help we can get."

"Alright." Silver acquiesced. "Just a few quick questions though... Who is Amy Rose? Where in Station Square should I look for her? How do I get her to believe me? Where on Mobius is Station Square? And, how do I know how to get back here when I'm done?"

* * *

A short walk, and a plethora of answered questions later, Silver the hedgehog jumped from the edge of the floating island and levitated toward the coast of the mainland. Tails followed close behind, twirling his namesakes as he soared through the air. They would go their separate ways once they reached land, but would meet up again at the end of the day before returning to Angel Island.

 _Go find a few detectives and an obsessed girl, they said. That will really get our resistance started._ Silver shook his head in disbelief as he glided through the clouds. _I guess it's not like I have a better idea at this point._

A few minutes later, they reached the mainland, and Silver waved goodbye to Tails as the kit flew down toward the rurns of Westopolis for his scavenging work. _I hope he doesn't get into any trouble down there._

Turning his focus back to his own task, the white hedgehog willed himself to go faster, and a sonic boom resounded over the landscape as he shot off to the east.

The mountains he had climbed the day before passed by underneath him, and the wide open plains he had first arrived in were spread out before him. It seemed like so much longer than a day and a half, in his view. So much had already happened to him in this world. Finding out that Sonic, the hero he was sent to look for and help, had already been defeated. Meeting Tails and Knuckles, forming a fragile resistance with them. Experiencing the natural beauty of a non-ruined world. Even now, he was on his way to meet new people and see new places.

 _Never a dull moment._ He reflected wonderingly.

The long miles of flatland passed quickly beneath the supersonic hedgehog, eventually giving way to another mountain range, beyond which lay the fertile eastern coastlands that Station Square was settled in. The city was one of few left on Mobius with a mostly human population, and was packed with tall and proud buildings that were yet untouched by Eggman. It was another amazing and unfamiliar sight to Silver. Levitating down, he perched himself on the edge of a skyscraper, and took in the sight of it. Late morning sunshine beamed down from a clear sky, and reflected off the gleaming structures all around. The atmosphere was calm and warm, with just a hint of salty sea air wafting over from the coast. All in all, it was quite a beautiful day.

Unfortunately, however, the happy and tranquil atmosphere above contrasted greatly with the scene on the ground. Civil unrest infected the whole city like a virus. People thronged on the streets, many dressed all in black as they mourned the fate of Sonic and Westopolis, others besieging the news stations or government buildings, searching in vain for a solution to the problem Eggman now presented. Some crowded into the plazas and parks, or popular street corners, protesting angrily against Eggman or foretelling "the end of the world".

 _What a mess!_ Silver looked down at the scene in dismay. _How am I supposed to find the Chaotix or Amy through all of this?_

Shaking his head, Silver levitated down from the building, hovering over the restless crowds thronging through the street. _Might as well start somewhere._

"Hey!" He yelled over the din of the masses.

The noise lessened as a portion of the crowd looked up, staring at the flying hedgehog in fascination.

"Ummmm..." Silver began awkwardly. "Can you- can anybody- tell me where the Chaotix detective agency is?"

Most of the throng shrugged or looked questioningly to their neighbor, but several arms lifted and began pointing down the street. "Three blocks down, one to the left!" Yelled somebody.

"Thank you!" Silver shouted back, turning to quickly fly down the street, leaving a confused and wondering crowd behind him.

* * *

The Chaotix detective agency occupied a small, rather run-down building just outside of downtown Station Square. A faded sign on the front of building boldly proclaimed: "We'll take any job that pays!"

Silver stared at it in slight disbelief as he dropped down to the sidewalk. "Sure doesn't look like much _."_ He muttered to himself, before walking up to the door. It was locked, and the window blinds were closed inside.

 _Great. Just great. Now where do I go?_

A moment later, he suddenly felt a tap on his shoulder. Jumping slightly, the hedgehog turned around to find himself face to face with an expressionless purple chameleon, twirling a shuriken star between his fingers.

"What brings you here, stranger?" The chameleon asked searchingly.

"I'm here to talk to the Chaotix." Silver replied, keeping a wary eye on the ninja-star. "I need their help."

The chameleon raised an eyebrow at this. "Come with me, then." He produced a key, quickly unlocking the door and leading the way inside. The room was dark, and somewhat musty, and there were multitudes of files scattered haphazardly about the floor. The only furniture pieces were a half-open filing cabinet in one corner, and a large desk toward the far wall. Behind the desk sat a large crocodile with a gold chain around his neck, wearing a pair of clunky black headphones and nodding his head to the beat they pumped. Silver had barely stepped foot inside, however, when he was forced to rear back as an orange-vested honeybee wearing a pilot's helmet and goggles appeared only inches from his face.

"Who's this guy?" The bee questioned in his high-pitched young voice.

"I'm Silver..." The hedgehog answered, rather unnerved at the sudden invasion of his personal space.

"Charmy!" The crocodile yelled in a gravelly voice, noticing his guest visitor for the first time. "Give him some space!"

Silver nodded in thanks, taking a quick glance at each of the three extremely diverse beings in the room before opening his mouth.

"I assume you three are the Chaotix?"

"That we are." The crocodile said with a grin, standing up and offering his hand to Silver. "I'm Vector. That's Espio back there. And I know you've already been acquainted with Charmy Bee."

"Silver the Hedgehog." he greeted, shaking the hand offered to him. "I'm here to ask for your help."

Vector leaned back in his chair, studying him, as Espio watched silently from the corner and Charmy flew around in lazy circles.

"What kind of help?" The crocodile asked. "And how much does it pay?"

"It doesn't exactly pay in normal terms..." started Silver. "I'm here on behalf of Knuckles the Echidna."

Vector raised an eyebrow at the mention of the guardian. "Knuckles, you say? We haven't heard from him in ages. This is about Sonic, isn't it?"

"In part, yes. How did you...?"

The crocodile jerked a thumb to the closed and shuttered window. "The angry mob outside is there for a reason. The defeat of Sonic is nothing to sneeze at, and it's no coincidence that Knuckles contacts us now. If you know that echidna, you'd know he doesn't socialize unless it's necessary."

Silver nodded. "Well, you're right. I am here because of Sonic's defeat. In his absence, Eggman poses a greater threat to this planet than ever before. Knuckles is forming a resistance to fight back, and we need all the help we can get. He said he could count on you to have his back." Looking Vector in the eyes, he continued: "I know it doesn't technically pay you, but the fate of the world is in the balance here. If we don't fight back and stop Eggman, the world will burn, and it will never recover. Believe me, I know."

Vector studied him closely for a moment, then stood up. "Well, if the fate of the world hangs in the balance, I guess there's not really much choice, is there?" He looked to Espio for a moment, who nodded his approval. Then he looked over to the other member of his team, who was busy doing loop-de-loops in midair.

"Charmy!" He yelled. "You wanna go help Knuckles fight Eggman?"

The bee zipped over to the desk, giving a thumb's up. "Whatever you say, boss!"

Silver smiled as Vector turned back to face him. "Sign us up then." The croc confirmed with a smirk. "It'll be just like old times."

"Thank you." The hedgehog said sincerely. "Pack whatever food and supplies you can, Knuckles is a long way away, and everything will be useful up there."

Vector nodded. "Charmy, get ready to lock up the building. Espio, let's get busy packing."

"One more thing..." Silver began as the Chaotix started bustling about to get ready. "I'm looking for another person while I'm here in this city. I don't suppose any of you know where Amy Rose lives?"

* * *

10 minutes later, Silver stood outside an apartment on the third floor of one of the skyscrapers downtown. He raised his hand to knock, and it wasn't long before a muffled and slightly hoarse voice yelled "Go away!"

 _Well, that could have gone better._

"Amy Rose?" He asked questioningly toward the door.

There was silence for a moment before the voice answered again, sounding much closer. "What do you want?"

"I need your help." He responded. "I was sent here by Tails and Knuckles."

At the mention of the fox and echidna, the door swung open immediately, revealing a young pink hedgehog in a red dress. Her emerald eyes were bloodshot and her cheeks were wet with tears. "What did you say?"

"Uhhhh... Tails and Knuckles sent me." Silver repeated, caught off guard by her distraught appearance. "Are you... alright?"

The pink hedgehog girl looked at him questioningly for moment, then realized what her face must look like, and quickly wiped away her tears. "Oh, no... I mean, I'm not hurt or anything. It's just not knowing where Sonic is..." She said with a sniffle.

"Right..." Silver remembered a warning Tails had given him before he left earlier. _"Be careful, she might not be in the best mood right now. She's very... attatched... to Sonic."_

He took a deep breath before continuing. "I hear you were... quite close to him. I'm sorry he's gone."

Amy nodded, before speaking quietly: "I know he's not dead. I don't know where he is..." She sniffed. "Or if he's hurt... but I know he isn't gone. I just know it."

Silver put a comforting hand on her shoulder. "I can't help you right now with what happened to Sonic. He was still alive the last time anybody saw him, but not even Tails knows for sure how it ended. If you come with me though, I can help give you a chance to find out someday." Amy lifted her head to look at him, as he continued: "I'm here to tell you that we're forming a resistance to fight back against Eggman, and we're asking your help. If we find Sonic alive, we'll do everything in our power to rescue him. Otherwise, we'll fight Eggman on our own, with everything we've got, and we'll make him pay for what he did."

Amy nodded determinedly, wiping her face again. "I'll do it. I'll do anything."

"Good. Pack whatever you need, whatever you can carry, and I'll take you to Knuckles and Tails after we meet back up with the Chaotix."

"The Chaotix?" Wondered Amy as she started moving about her apartment to pack. "They're coming along too?"

"Yes. They're why Knuckles sent me to this city in the first place, actually. Tails insisted I try to find you while I was here."

She smiled. "Tails is a good kid." Then she paused. "How's he taking everything?"

Silver sighed. "He was in pretty rough shape when I found him yesterday morning. He had to flee to save himself, leaving Sonic behind at the mercy of Eggman's henchmen. He's been better, though, since he got some rest and has something productive to do now."

"That's good." Amy nodded her head in approval, quickly getting back to work. "By the way..." She added. "You never told me your name, or how you got involved in this."

A corner of his mouth lifted wryly. "My name Silver. And as for how I got involved here, well... That's a rather long story."

* * *

One paradoxical and time-traveling explanation later, Silver made his way out of the apartment building, with Amy following at his heels and dragging a suitcase behind her. "What's all this?!" She cried, stopping short at the sight of the civil unrest on the streets in front of her.

"Apparently, you're not the only one upset over Sonic's disappearance." Silver replied. "You didn't know about this?"

"No, I haven't been out of the apartment since I heard the news..." She looked out over the thick crowds. "How did you even get here through all of that?"

At this, Silver couldn't help but chuckle. "I cheated." He grinned, as Amy looked at him questioningly. The cyan lines on his glove palms and bracelets glowed bright, and he levitated himself into the air as Amy watched in wonder.

"You can fly?" She gasped in delight.

"It's more like moving myself with my mind." he answer as he hovered. "But you can call it flying." He held his palm out toward Amy, focusing his power as a cyan glow surrounded her. "You don't mind going fast, do you?"

The girl simply laughed. "I love going fast. I have to, if I want to keep up with Sonic!"

Silver grinned. _She's weird, but she's nice._

With a quick telekinetic push, they were off, soaring through the warm air over the city, faster than anybody in the streets below could track. In no time at all, they were back at the Chaotix agency, hovering above the three detectives who stood outside with backpacks on.

"Ready to go?" The white hedgehog asked, as Amy waved in greeting.

Vector gave a thumbs up, and Charmy jumped into flight. Reaching toward the crocodile and chameleon with his free hand, Silver floated them into the air. In a moment they were all flying off to the west, with Silver maintaining a strong telekinetic hold on his passengers, and Charmy buzzing close behind.

As the afternoon sun beamed down from above, Silver looked from one new ally to another, considering them. Amy had closed her eyes, and was smiling as she enjoyed the feel of the wind on her face. Charmy was happily dancing around in the air as he flew, bobbing and weaving with an occasional loop-de-loop thrown in. Vector was gesticulating enthusiastically as he and Espio had a chat about something, but Silver couldn't quite hear what was said.

 _They're an odd bunch, that's for sure._ The hedgehog contemplated as he surveyed them. _But they're good people. Vector and Espio look like they could definitely hold their own in a fight._ He turned his face back ahead to the west. _Besides. Any pair of hands to help will be useful._ His thoughts turned back to the morning discussion with Knuckles and Tails. _This morning we were only three. Now, we are seven._

 _At the very least, it's a start._ Silver reflected with a small smile. Giving a mental push, he increased the group's flight speed, anxious to reach Angel Island before sunset.

* * *

 **Author's note: Sonic canon is all kinds of messed up. Some games take place in a world where humans exist (Adventure 1/2, 06, Shadow, Unleashed), and some games like Heroes or Forces don't have any except Eggman. I referred to Station Square having a mostly human population, because in the games, it does. I know Forces didn't have any humans in it besides Eggman, but if Shadow is here, then the ARK exists, Maria existed, and GUN exists. Which means humans (beyond Eggman) exist in this world. So this story will work kinda like the comics used to, where the planet is called Mobius, and humans exist alongside the anthropomorphic animals. Hope that makes sense.**

 **Anyway, like I said earlier, this chapter is less intense. Not really any action here, because I wanted to put some focus on getting the main leaders of the resistance together, and show Silver's first meetings with them.**

 **A quick note on the newest members of the resistance:**

 **I like the Chaotix. I know some people don't care for them, or find them annoying, but they add a unique and fun element, and I think they're largely underrated. That being said, I'll bet we can all agree that Charmy's lines in Forces were just... *cringe*. Charmy isn't going to be that bad in this story, if I can help it at all, lol.**

 **And Amy Rose... She's the hardest to write here, because her character has changed so many times over the series. She used to be more of a tomboy, and a bit crazier in her affection for Sonic than she is now. She also doesn't have her own adventures or fight as much as she used to in games like Adventure or Heroes, though we did see her fight very briefly in Forces. Also, she's usually pretty happy and outgoing when we see her in the games, but here I wanted to show a different side - what she'd be like in the immediate aftermath of Sonic's defeat. So I hope I didn't mess her character up too bad, though in** **all honesty, we'll probably be seeing a more mature side of Amy for most of this story.**

 **(And before anybody asks, this is not a shipping fic. If you're looking for a Sonic/Amy fix, you probably want to be elsewhere.)**

 **As always, suggestions/opinions/reviews are welcome, and I'll have the next chapter (with a bit more action) posted for you soon!**


	9. Uninvited Guest

**Alright, chapter 8 is finally here! Thank you again to all my reviewers and followers.**

 **bajy \- Cream likely wasn't in the game just because they already had so many characters in the story, and she wouldn't add much since they already had Charmy there to play the "innocent little kid" part. Cream is also an issue because several of the games she's played major roles in (Advance series, Rush, Chronicles) don't fit in with the main game canon(s). I don't think she's even appeared at all since her minor role in Generations. **

**Awdures \- I'm glad you liked it. I felt it was important to give Silver his own little introduction to all the new faces. His is by far the most unique viewpoint to write from. **

**MobiusHero \- I try my best, and I'm happy you're enjoying it so far. I've got no intention of ever giving up on it. So don't worry. (Even if life does make updates a little slow once in a while.)**

 **And now...**

* * *

Chapter 8 - Uninvited Guest

* * *

Knuckles watched from the rocky edge of his island as Silver and Tails glided off into the mists below, to begin their appointed tasks for the day. Once they were out of sight, he turned around and headed back into the thick jungle. The sky above was perfectly clear, the morning air was cool and fresh, and the island was blessedly peaceful, just the way Knuckles liked it.

 _It's not going to remain peaceful for long though._ His thoughts reminded him sourly. _You just lent it out to a freaking army._

The echidna shook his head at the thoughts. His task for the day, foraging food, was a simple and easy one - by design. It kept him on the island, close to the emerald, and it allowed him time to think in peace about the war he had suddenly been thrust into.

 _It's not like I had much of a choice._ He reminded himself as his shoes trod the damp soil of the jungle floor, walking between grape vines and fruit trees. _I know I can't sit this one out. At least this way, I'll be able to stay here with the emerald while organizing the resistance against Eggman._

The guardian was never one to cower in the face of a threat, but even he was worried about how this struggle would end. Eggman, with his gang of new and old villains, posed a more serious threat now than he ever had before. Defeating Sonic the Hedgehog was no small feat. The echidna knew that better than most, having faced off against the hedgehog personally in the past.

 _To make things worse, we don't even know who we're facing._ Knuckles lamented to himself as he worked. _So much of this makes no sense! Who is the masked one? What makes him so powerful? And why is Chaos back?!_

That last question bothered Knuckles more than any other. The last time Chaos appeared, the Master emerald had been shattered, and Station Square had been all but wiped off the map. If not for the intervention of Sonic as he utilized all seven chaos emeralds, the catastrophe would have been far worse. Chaos was angry and vengeful then, but that issue had been solved, hadn't it? For what reason had it returned? Was it after the chaos emeralds again? The guardian only had one of them on the island, the other six could be anywhere.

 _There's another thing to add to the Resistance to-do-list._ Knuckles mused. _Find all the chaos emeralds, and find them fast. I'm sure Eggman is after them too, and who knows how far he's gotten already._

Suddenly, the guardian's ruminations were interrupted by the unwelcome feeling the he was no longer alone on Angel Island. But Tails and Silver weren't supposed to be back for hours, at the very least. The Master Emerald needed him.

Dropping the sack of fruit he had collected throughout the morning, Knuckles dashed toward the shrine. Weaving and ducking through shortcuts in the underbrush that only he knew, jumping and gliding over ravines and creeks, he quickly made his way to the shrine at the heart of the island. The emerald was still in its place, untouched, but the feeling of an intruder on the island was getting stronger. The guardian closed his eyes, taking a deep breath and concentrating.

 _It's definitely not Tails or Silver._ Knuckles deduced. _But whoever it is does feel familiar somehow..._

Violet eyes snapped open, as the identity of the intruder hit him. _What is_ she _doing here?_

Not waiting to find out, the guardian concealed himself in the jungle near the shrine as the intruder drew ever closer. Soon enough, a gentle flapping of wings was heard, and a pair of heart-tipped white boots touched down at the top of the shrine. Rouge the bat looked searchingly out toward the jungles for a few moments, then turned toward the emerald, surveying it.

Knuckles didn't know why she was here or what she was doing, but given her history with the emerald, he wasn't about to trust her. _Especially_ since she spent a lot of time with Shadow, who only a couple days ago had helped attack Sonic and Tails. Maybe she wasn't a part of that. But the echidna always preferred to punch first, and ask questions later.

The guardian leapt from the jungle towards the bat, who noticed him a split second too late to dodge, and tackled her roughly, sending them both tumbling down the steps of the shrine. Rouge kicked him away quickly, and they both faced off against each other. Knuckles, with fists raised and teeth bared, moved quickly to position himself between her and the shrine. Rouge simply dusted herself off and put a hand on her hip.

"That wasn't a very warm welcome." The bat remarked with a sly grin. "Hardly the way to treat a lady."

"I hardly think you qualify as a lady." The echidna firked back, not dropping his guard.

"Oh please." Rouge laughed. "You hardly think at all."

The guardian growled, lunging forward with a right hook. His quarry ducked beneath it, her leg kicking out and sweeping his from under him. He landed hard on his back, before quickly rolling to the side as Rouge sent her foot toward him. Jumping back up, he threw several quick fists at her, each of which she narrowly dodged to the side of.

"Getting slow in your old age?" The bat taunted, jumping into the air and aiming a roundhouse kick at him, narrowly missing his head as he ducked.

"You wish." Grunted Knuckles, hurling a spiked fist. Rouge twisted aside, and landed a kick to the guardian's side. He recovered quickly however, and his next punch only missed by a hair. With a flap of her wings, the bat leapt over him, and sent a kick at him from behind. But the echidna was faster, ducking beneath her boot as it sailed over his head, and landing a powerful punch to her side.

Rouge was sent flying by the force of the blow, landing with a grunt against the steps of the emerald shrine. "Not bad." She conceded with a wince, starting to get up.

Knuckles watched her carefully, knowing there was still a lot of fight left in her. "Why are you here?" He demanded as he stepped closer, fists raised threateningly.

"To talk, not to fight." The bat replied, looking him in the eyes.

The echidna snorted. "I find that hard to believe."

"Hey, _you_ jumped out and tackled _me_." Rouge pointed out, raising her voice slightly. "Don't go blaming me for the fight when you're the one who started it!"

"You're the one who was nosing around the Master Emerald!" He snapped back.

"I was looking for its brainless guardian!" Came the frustrated rejoinder. "Where else was I supposed to look?"

Knuckles was already in a bad mood, and the insult only added fuel to the fires raging in his eyes. "I'll show you brainless!" He growled, charging at the jewel thief again.

Rouge grit her teeth and rolled to her left, kicking aside the fist hurling towards her, and slipping into a battle stance once more. Another fist missed her head by an inch as she dodged to the side, before darting into the air and throwing a series of kicks at the guardian in return.

Knuckles ducked under the first powerful kick that swept towards his head, and deflected another blow as he stepped backwards. Her third kick was short, and the forth was stopped by a powerful spiked fist. Then she darted to the side, tossing a fist at the side of his head. He blocked it, but left his chest partially exposed, a mistake he soon paid for as a harsh kick sent him stumbling back. The echidna chided himself for the error, shaking off the hit as Rouge rushed him again.

He had barely gotten his fists raised when the bat collided with him, knocking him onto his back. Grabbing her arm as she threw a fist at him, Knuckles yanked the batgirl down and rolled above her, forcefully restraining her.

The jewel thief only smiled seductively from beneath him. "Why Knuckles, I'm flattered." She said with a sultry voice, batting her eyelashes. "But you should at least take a girl out to dinner first."

The guardian's muzzle turned as red as his fur. "That- you- I wouldn't-" He spluttered out angrily, as his grip momentarily loosened. Rouge took quick advantage of his flustered behavior, breaking out of his grip and kicking him away.

 _I hate it when she does that._ Knuckles scowled as he stood up, watching the bat smirk at him. Resolving not to let her distract him again, he raised his fists and crouched defensively as she circled him, preparing to attack.

The female was slightly faster, and definitely more agile, but he was still the stronger one. He would wipe that smug smirk off her face.

Rouge darted towards him, and he stepped back with one foot, letting her kick fall short. He threw a quick jab at her, but she dropped quickly beneath his fist. Jumping the sweeping kick she sent at his legs, he quickly went on the attack, sending a series of powerful swings towards her. She was forced back by the assault, and tried to lunge sideways away from the blows. The guardian saw an opening, and immediately swung his foot out, catching the bat in her stomach. She grunted and fell backward, but Knuckles wasn't going to give her time to recover. He jumped at her, and she managed to roll away into a crouch, but was immediately hit by the next powerful fist sent her way.

Rouge was knocked back, down onto the dirt, and this time she made no move to get up. The guardian stood over her with his fists still raised, as she groaned painfully.

"You know..." She muttered, with a hand on her injured stomach. "I'm starting to get the idea that you really don't enjoy my visits."

Knuckles rolled his eyes. "Maybe it's because I like the emerald safe, and where it belongs." He responded bitterly.

"I'm not here for your stupid emerald." The bat replied tiredly. "I told you I'm here to talk."

"Then why didn't you lead with that when you first got here? I know you were spoiling for a fight." Accused the echidna.

The bat snorted, slowly getting up. "We both know, Knuckles, that you're seldom willing to talk without a good fight first."

"Well excuse me for being suspicious of the treasure hunter standing so near my emerald!" The guardian defended.

Rouge glared at him, despite her injuries. "That's _not_ why I'm _here_!"

"Oh, right." The echidna retorted with biting sarcasm. "You're just here for a friendly chat!"

"No, I'm here about Sonic!"

There was a long silence that followed. The only sounds were the chirping of birds and the rushing of wind over the leaves of the surrounding jungles, as the bat and echidna stared each other down. Ever so slowly, Knuckles lowered his fists. _What does she know?_ He wondered to himself. _And who's side is she on?_

"What about Sonic?" He inquired suspiciously after a moment.

Rouge sighed deeply, shaking her head. "Anything you know." She replied.

The guardian raised an eyerbrow.

The bat continued. "Technically, I'm here on behalf of GUN. Truthfully, I need to know for myself. The public very obviously believes that Sonic is dead, but nobody really knows for sure what happened to him." She shook her head. "I would ask Tails, but nobody knows where he is, so I figured I'd try my luck with you instead. Do you have _any_ idea what happened to them, or are you completely ignorant up here on this rock?"

There was a period of silence before Knuckles answered her. _Is she really here on behalf of GUN, or is she still working with Shadow? I still don't trust her enough to tell her anything._

The guardian crossed his arms. "Why should I trust you?"

Rouge narrowed her eyes, and pointed a finger at him accusingly. "You know something, don't you?"

The echidna was silent, continuing to stare distrustfully at her.

"Why _wouldn't_ you trust me here?" The bat asked frustratedly. "I'm no big fan of the Egghead, and neither is GUN. I'm on your side here."

"And what about Shadow?" Knuckles questioned. "Wherever he is, you're never very far behind."

At this, Rouge looked deeply troubled. She fiddled with her gloves as she answered: "Shadow is... He's gone somewhere I can't follow. I don't know what's happened to him." She shook her head despairingly. "He and OMEGA were on a private mission to one of Eggman's facilities, several days ago. OMEGA was in serious trouble, and Shadow went in after him. Shortly after that, I lost contact with them."

Knuckles listened intently to her narrative, as she continued: "The next morning, Eggman attacked Westopolis. I barely made it out of our HQ before it was blown to pieces, and when I made it outside, Shadow was there. He attacked me. Without any explanation, without answering when I asked him why, he just viciously attacked me. I had no choice but to fly out of there as fast as I could. Next thing I know, the news is reporting Sonic's defeat, and Shadow's participation in it."

Her eyes were slightly watery now, as she spoke of the experience. "I don't know why he did it. It doesn't make sense! Why would he betray me like that, Knuckles? I've never done anything to hurt him!"

It was true, the guardian reflected. Rouge had always been by Shadow's side - always been his ally, if not necessarily his friend. Any other time, he would have found it very hard to believe the bat's story. But just yesterday, Tails had testified to him about the defeat of Sonic and the return of Chaos. So pretty much anything was believable at this point.

"I don't know, Rouge." He finally responded. "But a lot of things don't make sense lately."

Gesturing for her to follow him, Knuckles climbed the steps of the altar, taking a seat at the top to rest.

"Tails came here yesterday." The guardian confessed, as she sat down next to him. "He brought a hedgehog with him. Not Sonic, but a white hedgehog - from the future."

"The future?" Rouge expressed incredulously.

"You don't have to believe it. But I do. He showed me a note that I wrote - or would have written, seven months from now. In it I explained that Sonic was defeated, Eggman had taken control of the whole world, and I was forcing myself to exhaustion trying to keep the Angel Island hidden."

Rouge leaned in to listen with mounting interest, and Knuckles sighed as he continued. "In that timeline, I was forced to take drastic steps to insure the safety of the emerald, and Angel Island was lost for centuries while Eggman's empire ruled the world with an iron fist. The planet was polluted and ruined over that time, to the point where life was barely sustainable. That's when Angel Island and my note was found. Using the information in the note, Silver - the white hedgehog, came back in time to save Sonic and prevent Eggman from even creating his empire in the first place. But he was a little late."

"What happened to Sonic?"

The guardian shook his head. "Eggman doesn't only have Shadow on his side. Other villains from Sonic's past showed up, including Chaos somehow."

"Chaos?" Rouge muttered in bewilderment. "I thought that problem had been taken care of years ago?

"Join the club." Knuckled grumbled. "Anyway, Sonic was faced with Shadow, these villains from his past, and a powerful new masked being we don't know anything about. He never stood a chance. He told Tails to flee for his life."

"Could he still be alive?" The bat questioned.

"Who knows." The echidna answered. "If he is, it's only because Eggman didn't want him dead."

Rouge looked down at her feet sadly. "What are we going to do without him?"

Knuckles hesitated for a moment, before answering. "Tails, Silver and I are forming a resistance to fight back. Tails is scavenging the ruins of Westopolis for parts to build communicators and security systems. Silver is on his way to get Amy and the Chaotix, and then bring them back here."

"Back here?" Rouge asked in disbelief. "You're setting up a resistance _here_? On Angel Island?"

"Its more like I'm _leading_ a resistance on Angel Island." Knuckles grumbled. "It was the only way I could be a part of this and still keep the emerald safe."

"Awww, this means a lot to you, doesn't it?" The bat teased with a grin.

Knuckles rolled his eyes, giving the bat a half-hearted shove for her teasing. "Yeah, yeah, laugh it up." He said, with a shake of his head. Then he spoke seriously: "In truth though, it means more to me than you can imagine, Rouge. That note Silver brought from the future... It made me realize I can't sit this one out."

Rouge studied him in silence for a minute, then nodded.

"I can't sit this one out either." She announced. "If you're serious about this resistance, you'll need all the help you can get."

She paused in thought for a moment, before continuing: "GUN knows that you and Tails have helped Sonic save the world several times over. I'll bet I could get them to offer your Resistance some support in this fight. We're on the same side, so why not work together?"

Knuckles sat and contemplated the idea for a minute, as a gentle wind blew over the shrine. _It might not be such a bad idea_. He thought. _As long as GUN doesn't try to order me around on_ my _island._ He looked briefly up toward the sun, still hanging high in the midday sky.

"That might be a good plan." He finally said. "But I want to talk it over with the others first, when they get back."

Rouge feigned shock. "Who are you and what did you do to Knuckles?" She demanded. "You're sitting here, calmly thinking things through, and you also just admitted that I had a good idea!"

Knuckles flushed in embarrassment. "I said _might_!" He growled. "You _might_ have had a good idea!"

"Aww, it's okay." The jewl thief teased with a sultry smirk. "I know how you really feel."

"Ok, that's it batgirl!" The echidna shouted with a swing of his fist, and Rouge jumped back, laughing as he tried to attack her again.

* * *

A couple hours of teasing, arguments, and half-hearted fighting later, Knuckles ended up draging Rouge with him while he finished his food gathering for the day. No way was he leaving that thief alone anywhere near his emerald. The guardian worked at that (with some reluctant help from Rouge) throughout the remainder of the day, until the lengthening shadows made further gathering impractical.

The sky was darkening in the east, and the radiant disk of the sun was nearly touching the western horizon, when Knuckles finally sensed the approach of Tails and Silver, along with the newest members of the Resistance. A few minutes later, he stood on the rocky edge of the island to greet them, with Rouge still close enough to keep an eye on. Tails landed first, breathing heavily, but smiling and carrying a heavy sack of mechanical and electrical components.

"Hi Knuckles! And... Rouge?" The fox greeted with his head tilted in confusion. "What are you doing here?"

"Rouge came to learn about what happened to you and Sonic, and to offer us some potential help." Knuckles answered before Rouge could open her mouth. "We'll discuss it as a group later. Any trouble down on the surface?"

"Nope." The kit reported. "I stayed well out of sight, and only scavenged on the outskirts of the ruins."

"Good." The echidna nodded approvingly.

Just then, Silver appeared from below, along with his passengers. The telekinetic glow faded as the group landed, and Silver took a deep breath, a bit worn from using his powers all day.

"Knuckles!" Charmy cried, zipping towards the guardian excitedly. Despite flying all afternoon without stopping once, the young bee still somehow had boundless amounts of energy. The echidna allowed a small smile in response to the exuberant greeting, and said his simple hello. Vector and Espio followed closely, the crocodile shaking the guardian's hand with a grin, and the chameleon simply giving a respectful nod. Amy offered a cheerful wave, and then headed over to greet Tails.

Knuckles surveyed his newly expanded resistance, and nodded his head approvingly. They weren't the greatest fighters, but they believed in the cause. It was a start.

* * *

A short while later, the entire resistance gathered around a fire built at the foot of the emerald shrine. Rouge sat among them, after having been re-acquainted with everybody, or introduced for the first time in the case of Silver. Freshly picked fruit was passed around, and the group chatted idly, until Knuckles stood up and garnered their attention.

"You all know why you're here." He began gruffly. "With Sonic gone, Eggman's armies stand ready to ravage the world, unopposed. We must _not_ let that happen."

There were nods of approval all around, and Silver's eyes glinted in determination as he recalled the ruin of his time.

"All of us are here," the guardian continued solemnly, looking over the group, "because we are willing to stand in his way."

"It won't be easy, I can promise you that right now." The echidna warned. "Anything that can defeat Sonic so quickly, won't go down easy. But we're going to try no matter what, because whole world is at stake here."

The nods of approval were more vigorous this time, as he continued his speech. "Right now we are only a small group, but Rouge offered up an idea today that might give us an edge as we continue to grow our numbers." He gestured to the bat next to him, and she stood up to speak.

"If you want to stand a chance against the Egghead right now, you're going to need help." She announced directly. "I'll be returning to GUN first thing in the morning. They know what Tails and Knuckles have previously done on behalf of this planet, and with a bit of skillful negotiating," she continued with a sly smile, "I think they could be persuaded to offer you enough material and logistical support to really get this resistance started."

"What do you all think?" Asked Knuckles of the group.

There was a quick hum of discussion, but everybody seemed quite open to the idea. Tails quietly explained what GUN was to Silver, who quickly grasped the situation and offered his support, saying: "We could use all the help we can find."

Espio offered the clearest argument in favor of the idea, asserting reasonably that: "We know GUN is no friend of Eggman. The enemy of our enemy is likely the best friend we can hope for at the moment."

There was not much to be said beyond that, and so Knuckles gave Rouge permission to negotiate with GUN on their behalf, on the condition that no mention be made of Angel Island until the militaristic agency had agreed to help.

With that issue settled, the guardian offered only a few more short words to his fledgling resistance. "It's getting late, so everybody should hurry up and get some sleep. Tomorrow morning, we start our work in earnest. We have a world to save, and a friend to either rescue or avenge."

* * *

Early the next morning, before the sun had even risen fully above the eastern horizon, Rouge and Knuckles stood together at the island's edge. "Don't get into too much trouble, and make sure to take care of my emerald while I'm gone." The bat teased with a smirk, spreading her wings and leaping gracefully into the early morning air.

"Oh, just go already." The guardian huffed, crossing his arms and holding back his grin. "You won't be missed."

"You know that's a lie!" She called back playfully, diving and quickly vanishing into the clouds below.

Knuckles stood for a moment, thinking in silence. Then he turned and began walking back to where the other members of the resistance still lay sleeping. The sky was aflame with the brilliant hues of dawn, the calm air was cool and invigorating, and the verdure all around him was wet with freshly settled dew.

The echidna breathed the atmosphere in deeply, and increased his pace. Morning was here, and it was time to wake the others.

 _We have work to do._

* * *

 **Author's note: In case you all haven't realized it yet, this is going to be a loooooooooong story. Here we are, 8 chapters and 30,000+ words in, and we've only gotten a few days past the defeat of Sonic. Granted, things will start to move faster pretty soon here, but still.**

 **Now to talk about this chapter specifically.**

 **We finally get to see where Rouge has been. One thing that bothered me about the game story was how Rouge was helping out the resistance from the beginning, but when Shadow shows up 6 months later, he acts like Rouge has been working with him this whole time too. Yet the resistance spends all that time thinking Shadow is evil, and Rouge never makes a comment. What gives?**

 **So in this story, Rouge isn't working with Shadow that whole time, and she thinks Shadow is working for Eggman just like the rest of the world does. I hope I didn't make her too out of character there, telling the story about what happened to her when Westopolis was attacked, but I wanted to give it a bit of a personal touch to her. She's always been by Shadow's side, and now suddenly he seems to have turned against her for no reason, and that no doubt stings emotionally.**

 **And I just want to say that I think Knuckles has been treated pretty unfairly by SEGA in recent years. He used to be intelligent, despite being rather gullible, but now he's largely treated as a dumb joke in the main games, to say nothing of what they did to him for Sonic Boom. So in this story, I'm trying to treat him a bit more fairly.**

 **Also, I love the dynamic between Knuckles and Rouge. (At least, the dynamic they had back in the SA2 days. Forces pretty much ignored it.) Those two are fun to write. They have a lot in common, but a lot of differences as well, and there's just so much tension between them, even though deep down they do like each other. So it should be fun to see more of that in the future.**


	10. Cruel Work

**Author's Note:**

 **Alright, sorry to keep you waiting folks, but here's the next chapter of _The Phantom War_. **

**As always, many thanks to my wonderful followers and reviewers.**

 **The Dragon Legend \- Don't be jealous, this thing is an intimidating beast to write! And longer isn't always better. :)**

 **TheLastoftheRealOnes \- Thank you so much for the kind words. Keeping the character's personalities faithful is one of the most important things to me, so your comment means a lot. **

**Mitha Sentro \- I'm glad you liked that Knuckles/Rouge interaction. Even though this is not a shipping fic, there will still be a lot of interaction and moments between characters like that. And who knows, maybe later it will lead to a short spin-off story or two about the characters, if there's interest in me doing something like that.**

 **Extreme Light 9 \- Well, I can tell you now that the Avatar character won't be a part of this story. You may see some minor original characters show up briefly to join the resistance later on, but they won't be a part of the main storyline.**

 **prowerboy \- Thanks! I've felt the same frustration over the way SEGA ignores past character development, so I'm glad you're enjoying this re-write. **

**Infinite's Ruby \- Thank you! The interactions between Knuckles and Rouge were really quite fun to write, and I'm glad to see it's been received so well. **

**Awdures \- It will be explored even more in later chapters, so keep reading! :)**

 **Now without further delay, here's the next chapter for you all.**

* * *

Chapter 9 - Cruel Work

* * *

 _He closed his eyes in acceptance of his fate. His power was drained, his golden fur fading rapidly to black. There was no sound, no air, nothing at all to be felt except for the interminable sensation of free fall._

 _He had given his all. The planet was saved. His goal... was it finally fulfilled? Was this the price demanded of him?_

 _Maria..._

 _This is what you wanted, right?_

 _This is my promise I made to you._

* * *

Shadow the Hedgehog awoke with a quiet gasp, glancing rapidly about his surroundings. The aged metal walls of the ARK greeted him in silence, and stars shown brightly outside the window of his small room.

Shadow sighed, rubbing a hand over his forehead as he got up from the old worn cot he had slept on. The black hedgehog had chosen to move on from his past after the Black Doom incident several years ago, and in most respects he had followed through with his choice. But ever since his return to the ARK, his dreams had been plagued constantly by troubled memories.

Shaking his head clear, Shadow strode from the room. It was only his third day aboard the space station, but already he was feeling frustrated. He had spent the last two days scouring the ruins of Westopolis for clues on what happened to Rouge. But it was an exercise in futility. No trace of the bat could be found anywhere among the rubble, and even the broken body of Omega had been stolen away by his creator's minions. Shadow now had no clue as to the whereabouts of either of his teammates, and his life was made even more difficult by the fact that he constantly had to remain hidden from robotic patrols, not wanting to risk crossing Infinite again unless he could find a way to effectively fight back.

The hedgehog's dark mood was only made worse by returning to the ARK to sleep each night. Everywhere he looked, he was assaulted with memories of the past. Visions of a young black and red hedgehog, curious and even hopeful, and so naively innocent it was embarrassing. Memories of scientists, and soldiers, and one beautifully kind young girl.

But those memories were no longer his. They belonged to a past life, one that had ended with a violent gunshot more than half a century ago. He was not that same innocent hedgehog. He had been reborn into the life he now led, and there could never be any going back. The past was the past, and Shadow was intent on leaving it there, where it belonged. Fate, of course, would never let it be that simple.

Steady footsteps soon brought the hedgehog into the ARK's power core, where his green chaos emerald lay slotted into a small alcove, powering the station's life support and lighting systems. A quick tug pulled it free, and the ARK grew dark and quiet once more. Shadow tucked the emerald into his quills, and turned around. Better to leave the ARK powerless than to leave a chaos emerald here unguarded while he went down to the surface each day. Besides, he didn't have a second one, and he needed a way to get down to the surface and back.

The dark hedgehog didn't even spare the ARK's halls a parting glance as he raised the emerald, feeling its familiar power flow through him. He was ready to be free again from the space station's cold metal walls, and the many memories held within them.

"Chaos Control!"

* * *

Barely an instant passed before Shadow found himself on the surface, standing upon a hill overlooking the ruins of Westopolis. The sun was just peeking over the horizon to begin its steady march up into the morning skies, and the atmosphere was still cool and calm. The city lay peacefully in its ruined state. There was no screaming or crying of civilians, no clamor of battle, no crackling of flames. The fires amidst the rubble had all completely burned themselves out, and the air above the city was still and quiet.

 _Too quiet._ Shadow realized, glancing around with a piercing eye. _Where are all the robots?_

The rubble was completely empty. It was devoid of all movement - all signs of life or activity. The past two days he had returned here, robotic patrols were plentiful, and had forced him to keep a stealthy and low profile. But now they were nowhere to be seen.

 _Where are they?_

With a silent scowl, the black and red hedgehog activated his hover-skates, and darted down into the ruins. His dark form was the solitary wanderer among the rubble. Not a robot was to be seen, except for the ones that lay broken and shattered among the collapsed buildings, destroyed by Shadow a few days previous, or perhaps even by Sonic, before his defeat.

Shadow slowed to a stop as he reached Team Dark's former HQ. Now nothing but a pile of collapsed concrete, wood, and glass. Here was where Rouge had last been heard from. Here, he had left Omega's shattered form alone, as he went on an angry rampage that accomplished nothing and nearly ended in disaster when Infinite arrived. Now, Shadow was alone, and there were no clues, no hints about where his teammates might be. Or even if they were still alive or not.

Gloved hands clenched into tight fists, and the hedgehog growled in anger and frustration. The Ultimate Lifeform had no problems with being on his own, but Rouge and Omega were still the closest things he had to friends, he was far from apathetic in regards to their absence. He was mad. Mad at Omega for mindlessly charging in and getting himself wrecked, mad at Infinite for doing the wrecking, mad at Eggman for causing the whole mess in the first place, and even mad at himself for not being able to save his allies. And on top of all that, the entire free world saw him as an enemy, because of Infinite's trickery. Everything about the situation was maddening and frustrating.

With an angry sigh, Shadow shook his head. This would get him nowhere. Taking a deep breath, he slowly reined in his emotion, before it grew beyond his control. Rage would do him no good right now. What he needed now was a new plan. Hanging around Westopolis any longer would be useless, and there were mysteries to be solved elsewhere.

 _Rouge and Omega are beyond my reach right now, if they're even still alive._ Shadow acknowledged to himself. _It's time to change tactics._

Two major questions faced the Ultimate Lifeform as he stood in contemplation amid the rubble, and he couldn't decide which was more important at the moment.

 _Where is the Doctor's army heading now? And how can I learn to defeat Infinite?_

After a moment of silent thought, Shadow decided to focus on the robotic army. It was, after all, the only question he could plausibly discover an answer to right away. Defeating Infinite was a more important goal overall, but there were no leads he could follow, and it seemed to be an out of reach goal for the moment. For now, there was a giant mechanized army on the loose, and even if the entire world hated him at the moment, he was still bound to protect it. For _her_ sake, if nothing else.

With a burst of power to his shoes, Shadow skated away, searching around the outskirts of the city for signs of the where the army had headed when they left. A large and powerful force of robots would leave unmistakable traces of its passing, and soon enough, Shadow found them. A large swath of ground had been completely trampled down, and multitudes of large deep footprints trailed away to the north - signs of the giant metal behemoths that had inflicted total ruin upon a once proud city. There was the trail to follow. Casting one last long glance at the wrecked city behind him, Shadow set his face in a grim line and turned to follow the enemy's track.

* * *

As the sun slid slowly through the midday sky, Shadow streaked in a dark blur over the landscape, in pursuit of Eggman's army. It didn't take the swift hedgehog very long to catch up to his quarry. The extensive army was marching northward at an unvaried pace, steadily traversing the small foothills along the coast. The spectacle of it was something to behold. An expansive silvery mass, glinting in the sunlight as it moved steadily over the hills. The ground itself shook at the impact of a hundred thousand metal footsteps, and the terrible sound of it could be heard from miles away. Eggpawns swarmed like insects around the feet of massive metal behemoths, and legions of buzz-bombers flew in rigid formations overhead. It was a great and fearsome horde of machines, built and dispatched for one solitary purpose - the subjugation of the entire world to Doctor Eggman.

Shadow slowed to a walk a couple miles from the large force, watching it from behind and endeavoring to keep himself hidden behind one of the smaller foothills. Even if he didn't have to consider the problem posed by Infinite, Shadow doubted he could take on the entire force by himself. For now he would wait, and watch, and plan.

 _This army is the largest I've ever seen assembled by the Doctor._ The dark hedgehog mused. _And unless they make a change of course soon, they must be headed straight for Metropolis._

The sprawling urban center of Metropolis, if it was indeed Eggman's next target, would still be a journey of several days at the robotic army's current pace. But there were a few small villages along the way, and Shadow knew they wouldn't stand any chance of survival in the face of this mechanized onslaught. With narrowed eyes watching the evil army, and arms folded characteristically over his chest, the Ultimate Lifeform considered his options.

 _It's not like I can fight off the entire army to protect those villages._ _But I can't go warn them to evacuate either. They don't trust me, they all think I'm working for the Doctor._

 _Perhaps it's better for me to just leave them to their fates._ Shadow reflected. _They wouldn't accept help from me anyway._

That was without doubt the easiest and simplest option. But try as he might to let that settle the issue, his conscience still nagged him, and his old promise weighed heavily on his mind. Words from the past resounded clearly within his head.

 _"Shadow, I beg of you... give them a chance..."_

The hedgehog shook his head at the recurring memory, but try as he might, he couldn't ignore it. He couldn't just leave those people to die, even if they did hate him at the moment. They were in danger, and he was the only being in a position to help them. He would have to do something _._

 _But what?_

What could he do to help villagers who didn't want him to help? He couldn't fight off an army that large, especially if Infinite was still leading it.

 _For that matter, my own replica could be the one leading it._ Shadow realized bitterly.

Immediately after that thought, inspiration struck him like a bolt of lighting. An idea presented itself, and Shadow knew what he would have to do. If the world viewed him as an enemy, then he would act like one. He would play off their fear of him, and send the villagers running from their homes. He would chase them out, and he would burn down their villages if he had to, but he could force them out of the army's path. They would be terrified, and they would hate him all the more, but at least they would live. And that was the important thing, wasn't it?

Shadow stared consideringly for a moment longer, watching the mechanical horde continue it's steady march. Then, with a face colder and harder than steel, he fired up his hover-skates and rocketed off toward the first village, taking care to remain hidden from the enemy.

* * *

Traveling just under the speed of sound, Shadow quickly and stealthily maneuvered around Eggman's army, reaching the first village only hour later. It was little more than a collection of thatched cottages, nestled among the hills. Mobian villagers were wandering about their daily lives, cooking or building, buying or selling, quite ignorant of the danger than was currently marching straight towards them.

Shadow stood unseen only a few hundred feet away, his crimson gaze wandering over the scene. The life these villagers led was a peaceful illusion. And he was about to shatter it.

"It's for their own good." Shadow muttered under his breath, as he opened himself to the power of the chaos emerald he carried in his quills. A moment later a stood, fists clenched and eyes blazing, at the edge of the village. Several mobians spotted him immediately, and stopped in their tracks. They knew who he was. _Everybody_ knew who he was. Chaos energy danced at his fingertips, and he marched slowly toward the village center. The normal bustle of life in the small community ceased entirely as he walked through it, and was replaced by a silent yet palpable terror. A family of rabbits stared wide-eyed from their doorway, and a female dog rushed into the street to drag a small child out of the Ultimate Lifeform's path.

The dark hedgehog stopped, glancing with narrowed eyes at the terrified faces around him. His expressionless face suddenly twisted into a furious scowl, and the villagers shrank back in fright.

"Leave. Now." Shadow growled, and the tone of his voice was enough to strike fear into the bravest heart on the planet.

Villagers stumbled back in their haste to get away as, with a fearsome yell that sounded more like a roar, the Ultimate Lifeform raised his hand and launched a massive chaos spear at the nearest and largest cottage. The powerful bolt of energy grazed the thatched roof of the building, setting it ablaze immediately, and its occupants quickly fled the building in a panic.

Shadow turned around, eyes sharp and teeth bared in a growl, with the flaming cottage behind him. Several citizens stood frozen in fear and awe as they stared at him, until he stepped toward them and roared angrily: "Leave!"

Nobody needed to be told again after that. Villagers fled in terror before the black and red hedgehog, harbinger of the destruction that awaited them all if they stayed any longer. Parents scooped up their screaming children and ran, and the elderly hobbled after them as fast as they could. Shadow strode menacingly through the streets, making sure every building was empty, every alleyway clear. He set buildings ablaze, or destroying them outright once he knew they had been evacuated. The inhabitants had to know, by whatever means necessary, that they could never come back to this place. Not with Eggman on the loose.

It didn't take long for the grim job to be finished. Soon enough, the little town was empty, and Shadow stood alone among the burning remains of homes and businesses. He watched as the last of the citizens fled over the hills to the east, then bowed his head. He had just taken away their homes, their livelihoods, their belongings. But he had saved their lives. Even now, his enhanced senses could feel the earth trembling under his feet, as the Doctor's robotic horde approached from the south. They would be here soon.

Shadow raised his head, and closed his eyes for a moment, steeling himself. Then, his hover-skates activated with a soft whine, and he shot off toward the next village. The mission was not finished yet.

* * *

Shadow's work at the second small town went much like the first. His reputation, as inaccurate as it was, preceded him, and the inhabitants once again scattered in fear before the powerful hedgehog. Street by street, house by house, he methodically set fire to the rooftops and drove the citizens out and away.

It was a terrible task, and not for the faint of heart, but it had to be done. Everywhere there were weeping children, terrified parents, mobians of every shape and size tripping over themselves in their haste to get away. They were being ripped away from everything they knew, and their lives would never be the same. But at least they would live to see tomorrow.

Shadow knew that somebody like Sonic could never have stomached this sort of work. He was too good, to _pure_ for a task such as this. But Shadow was not Sonic. Far from it. The blue blur could have been welcomed into the town as a hero, and warned everybody of the approaching danger. They all would have listened to him, packed up their belongings, and left. Shadow, on the other hand, could only be recieved with hatred, suspicion, and fear. If that was his lot, then that was what he would have to use to accomplish his goal.

So, as the last of the citizens escaped over the hills, and their town's buildings withered away amid wreaths of flames, Shadow the Hedgehog skated off toward his last target, anxious to complete the grim work.

* * *

The last village was slightly bigger than the other two, but Shadow wouldn't let that stop him. Darkness was falling as chaos energy set the first two buildings ablaze, and once again the Ultimate Lifeform roared out his demands:

"Leave! Or else!"

The simple threat was enough, and once again, the villagers fled. As the sun's last rays vanished beneath the western horizon, Shadow strode down the darkening streets, lit only by the flames spreading on the rooftops. He paced through houses and businesses, churches and markets, blowing holes in their walls and tossing any remaining inhabitants out onto the streets. The fires spread rapidly from building to building, and mass panic reigned amid the fleeing citizenry.

The hedgehog was nearly finished with his task of emptying the town when, in one of the last unvisited houses, he found a mobian child sitting alone in the corner. He was about to bare his teeth and scare the poor fool out of the building, when his eyes connected with hers, and something stopped him in his tracks. She was a young bird, only a few years old. Her feathers were grey, her blue eyes were wide and frightened. When she noticed Shadow, her innocent mind did not perceive a threat, and she instead reached out to him for help.

The Ultimate Lifeform stared for a moment at the youngling, and soon found himself unable to muster the will to scare her away as she reached out to him with innocent and pleading eyes. In that moment, his fight left him. The weight of all the terror and hardship he was putting these villagers through fell suddenly on his shoulders, and he couldn't gather enough anger to ignore it anymore.

Letting out a long sigh, he stepped over to the girl, grabbing her hand and helping her stand. He closed his eyes as the world flashed white, and a moment later they were on a hillside overlooking the burning town. The girl stared with wide eyes as her home burned, until Shadow nudged her shoulder, and pointed her in the direction of the other refugees. The young bird grabbed his hand, staring at him wide wide and frightened eyes, silently begging him to come with her. _To protect her._ But the hedgehog shook his head.

"I can't go with you." He spoke quietly, feeling an unfamiliar ache in his chest. "You'll be fine. Go find your family."

With that, he pulled his hand away from the girl, and gave her a gentle push toward the others. She turned, giving him one last mournful glance, and then ran off.

Shadow stared after her for a moment, with a disturbing pain in his heart. Then, with a flash of chaos energy, he was back in the city. He flashed from house to house, checking that all were at last completely empty, before retreating to a nearby hilltop. There, he watched in silent sorrow as the village burned. Even if it was for their own good, and it saved their lives in the end, he had still ripped three full communities away from nearly every material thing they had possessed in life.

As he sat down under the darkening twilight sky, staring at the destruction he had wrought, the last words of his dear sister rang through his head once more.

 _"Shadow... I beg of you... Give them a chance to be happy..."_

 _Well,_ Shadow couldn't help but think, _they certainly aren't happy right now._

Rage flooded through him, and he slammed his fist against the ground. But the anger left as quickly as it had come, and Shadow could only shake his head with a sigh.

 _Not everything is black and white._ He reflected tiredly. _It was either this, or they all die when Eggman's army shows up at their doorsteps. This way, at least they have a chance at survival. A chance at eventual happiness, however slim that chance is._

He paused his ruminations to look up at the stars shining above him. _That's all she ever really asked for, isn't it? A chance._

He looked back down at the burning village, then beyond it to the hill that it's citizens had fled over. _I'm doing the best I can, Maria. This world doesn't make it easy on me._

* * *

Shadow remained there on that hilltop, sitting in silence for the next several hours. Waiting for what he knew was coming. Soon enough, the ground began to tremble under the mechanized tread of mammoth war machines, and Eggman's army appeared, silhouetted against the dark southern horizon. Shadow watched patiently, as the robotic minions marched unwaveringly towards the now smoldering remains of the village. Once they arrived, the entire army stopped moving, except for a lone figure that hovered over the ruined town's center.

Crimson eyes narrowed as their owner watched intently from his perch. _Infinite._

The masked jackal hovered over charred and smoking ruins, examining the entire scene. Then he lifted his head, crossed his arms over his chest, and scanned the surrounding hillsides.

Shadow was on his stomach in the grass now, determined to remain unseen by his foe.

Suddenly, Infinite's unmistakable voice resounded over the landscape, impossibly loud.

"Just what do you think you've accomplished by all this, Shadow?"

The Ultimate Lifeform gritted his teeth, but remained silent and unmoving.

"You've burned down these three villages, and for what? Wherever the survivors are, they will be found eventually, and you can do nothing to stop it. Even if I don't find them, they will die of privation soon enough." Infinite paused to glance over the hillsides once more, but there was no sound or movement anywhere.

"You have accomplished nothing, except to make yourself even more hated by those you are bound to protect." Taunted the jackal. "They will perish hating you, and you will perish knowing that you are a failure!"

Shadow saw red, but through a supreme effort of sheer willpower, he remained still and silent.

Infinite remained silent for a long moment, before issuing his final taunt.

"You cannot win this war Shadow. No matter how hard you try."

With that, the masked jackal returned in silence to his army.

A few hundred feet behind him, a dark hedgehog raised himself up to standing. His gloved hand slowly reached into his quills, and removed the green chaos emerald. He stared at it in his hand for a moment, turning it over, then shifted his blazing red orbs to Infinite.

"It's not about winning the war." Shadow spoke quietly, but firmly. "It's about fighting the war, regardless of whether or not you can win it."

Infinite's head whipped around to face the sound, but he caught nothing more than a fleeting glimpse of the hedgehog, as he vanished amid the brilliant flash of Chaos Control.

* * *

 **And, that's it for chapter 9.**

 **Author's Note: This was a tough chapter to write. Much tougher than I expected. I'm pretty happy with the way it turned out though. Much better than what I had originally planned. We get some more insight into Shadow, and his struggles with his past and present.**

 **I wanted to explore Shadow, being truly on his own. Every ally he had is lost to him, the entire world is against him, he isn't the most powerful guy in town anymore, and he's always got Maria's promise hanging over his head. It's a lot for him to come to grips with.**

 **I also wanted to explore the antihero nature of Shadow here. We get to see him tread the fine line between right and wrong, good and bad. It's interesting to write, because while Shadow is definitely not as "nice" or "pure" as Sonic is, he's still motivated at his core by a promise to help others. He just goes about it in ways that other "heroes" would probably find unacceptable, because he used to be a villain, and because the world currently sees him as a villain.**

 **Anyway, it's a complex chapter that turned out way more intense that I originally envisioned, but I like how it ended up. And I hope you guys all enjoyed it as well.**

 **As always, any reviews or suggestions are very appreciated, and I'll talk you guys again in the next update.**


	11. The Enemy's Trail

**Author's Note: Sorry for the delay, it's been almost two weeks now since I've updated this. I wanted to get this chapter out quicker, but it got away from me and ended up being the longest and most difficult chapter I've written so far. Sigh.**

 **Anyways, thanks again to my wonderful reviewers and followers!**

 **Awdures \- Thank you. I really wanted to explore the anti-hero nature of Shadow here, in these situations where he's on his own, but I honestly wasn't sure how well that chapter would turn out. So I'm glad you liked it!**

 **Infinite's Ruby \- Thank you for the support! I'm doing my best to keep this story flowing for you guys, but hopefully I can pick up the pace of updates soon.**

 **Thanks as well to bajy and Extreme Light 9 \- I'm glad you're enjoying the story!**

 **Now on to chapter 10!**

* * *

Chapter 10 - The Enemy's Trail

* * *

Cyan energy blossomed in Silver's open palm as he held it out toward the solid rock wall in front of him. With a push of his mind, a telekinetic blast shot out toward the granite, causing it to crack and crumble. Another quick wave of the white hedgehog's hand, and the rubble was floating clear of the newly formed hollow, which was itself deep inside of a much larger cavern.

"That should be good enough for now." A pink hedgehog commented, as she carried a large sack of provisions into the new excavation and set it down with a sigh. "Thanks Silver."

"No problem Amy." He replied distantly, turning around to survey the day's work. What was formerly just a small cave that Knuckles had used for shelter in bad weather was now being expanded into a living quarters and storage area for the entire resistance. It was now a large cavern dug into the rock, branching off into several different rooms and passages. Some would be used for sleeping in, others would store provisions or weapons. There was even a room for Tails to store his scavenged parts in, which he was also using as a workshop of sorts.

After the departure of Rouge, Knuckles had set his confederates to work immediately, readying the island for its role as home base for the resistance. Tails made daily excursions down to the Westopolis ruins, so he could scavenge technical equipment, and Charmy joined him in the work. Amy and the other Chaotix were tasked with foraging food and creating a permanent habitation for the group. Knuckles had gone yesteday to move the Master Emerald to hidden palace, keeping it safely alone and out of sight. Silver himself had helped out wherever he could, foraging food or blasting away at cave walls, and even persuading the reluctant guardian to let him help move the emerald.

 _We've been hard at work._ Silver considered, folding his hand over his chest. _But we still have yet to begin our main task of fighting Eggman. We can't wait too long._

"Unless you still need me for something Amy, I'm gonna head out. I need to talk to Knuckles."

"Go ahead." The female replied, appearing at his side with another sack of supplies on her shoulder. "We're done excavating for the day."

Silver nodded at the girl, and strode back toward the surface. Reaching the mouth of the cave, he stepped out into a jungle that was almost completely obscured in mist. Angel Island had been flying hidden in the clouds today, and the dense fog that rolled over the island produced an almost ethereal atmosphere amid the tropical vegetation. _It's so unlike anything I ever saw in my time._ He reflected wonderingly.

Carefully following a path he had learned over the past few days on the island, Silver wandered through the cool evening mists and into the heart of the island. Reaching the emerald altar, which was now empty of its treasure, he circled the base of the shrine until he found what he was looking for - a well hidden stone doorway, easily opened with a small telekinetic push. A stairway led down into the bowels of the island, lit by dimly glowing crystals embedded in the walls. He followed it down to a large room, ornately decorated in stones of blues, purples, and greens, with various crystal formations lining the walls.

The room itself seemed to be a dead end, with no other ways to access or escape it. This was as far as Knuckles had let him come yesterday. After helping to bring the emerald down the stairs, he had been told to let the guardian go the rest of the way alone. The tone of the echidna's voice had brooked no argument, and Silver had returned to the surface.

Now, as he walked around the ornate room and ran his hand over it's smooth, unbroken walls, he wondered where and how Knuckles had gone from here. There was no gap in any of the walls, no sign of any doorway or passage. At his wit's end, Silver was ready to resort to opening his mouth and calling out for the echidna, when he was startled by a voice from behind him.

"What are you doing here?" Knuckles asked, standing in front of the staircase that the hedgehog had just walked down.

Silver gaped at the guardian. "H-how did you...?"

Knuckles shrugged. "That's for me to know, and nobody else to ever find out. Now what do you need?"

The hedgehog shook off his surprise at the guardian's sudden appearance, and replied: "I wanted to let you know that the supply cavern is almost finished. We already have enough food and water stored to last us all for a month, at least. Amy is moving in the last of it as we speak."

The echidna grunted. "She's been more helpful than I expected, considering what happened to Sonic."

Silver winced. "She's shed her fair share of tears over the past couple days." He replied empathetically. "But a good bit of work to focus on will help anybody forget about their other problems."

Knuckles nodded. "We've got plenty of hard work to be done, that's for sure. I think it's time for us to start hitting back at Eggman."

Silver nodded his approval. "I completely agree. We can't just sit up here forever. It's time we strike!"

"And the sooner the better." The guardian agreed. "Tails came straight here when he and Charmy returned from Westopolis this afternoon. He told me that Eggman's army is no longer occupying the ruins." Silver raised a curious eyebrow at this, as Knuckles continued: "The mechs must have left sometime last night or early this morning, but either way, Tails and Charmy didn't see a single active robot down there today."

"But where are they headed now?" The hedgehog asked concernedly. "We should have sent somebody after them to find out!"

"I thought about that." Knuckles confessed. "But I decided to hold off for today. Tails has been building communicators for us all, and he told me he'd have them finished soon. I don't like the idea of anybody heading down to the surface and facing off against that army without a way to contact the rest of us."

"Well I hope he finishes with them quickly." Silver replied. "Every second we waste, Eggman's army is marching unopposed somewhere on the surface."

"Why don't you go check on his progress then." Directed Knuckles, his arms folded over his chest. "If he can finish those communicators tonight, we can start chasing after Eggman first thing tomorrow morning."

"Will do, commander." Replied Silver, giving a nod to the echidna before heading quickly back up the stairs.

* * *

"Tails!" Greeted the white hedgehog as he entered the small room, littered with mechanical and electrical components. "How are the communicators are coming?"

The young fox looked up from where he was screwing something into place. "Almost done! I've finished flushing out the design, and I'm nearly done building the first one already." He said as he pointed to the small device he was screwing together. "It's not the best, but I did what I could with the parts we have. Eggpawns aren't exactly made from high-end materials."

"As long as we can keep contact with each other, it's good enough." Replied Silver with a wry grin.

"Oh! It can do more than that." The kit announced proudly, holding up the partially finished device. "Its a watch, first of all, so you can keep track of time. I've also built in a recording system, a radar, and a homing beacon. Its really..." He trailed off suddenly, staring blankly at the far wall.

"Tails...?" Questioned Silver. "Are you ok?"

The fox was silent for a long moment, before answering sadly. "Yeah, it's just that... The last time I made a communicator, and showed it off for somebody..." He sniffed. "It was for Sonic." A tear rolled down Tails' face as he continued: "Remembering that... It just made me really miss him..."

The white hedgehog put a comforting hand on his shoulder. "I'm so sorry Tails."

"I don't know where he is... I don't even know if he's still alive!" The kit sobbed brokenly.

Silver sighed, watching the crying fox for a moment before speaking: "I've never met Sonic. But I think I know enough about him to say, he'd be proud of you Tails. He'd be proud that you haven't given up, even though he's gone. And he'd be proud of the work you're doing now."

Tails sniffled a few more times, wiping his face with a gloved hand. "But what if he's really gone, Silver?" He cried. "What if we never find him? I don't know if I could go on, knowing I'll never... Never see him again..."

"You _will_ go on Tails, I know you will. You'll go on because we need you, because we can't let Eggman win this. And you'll go on because I'm sure that what Sonic would want for you."

The young fox straightened slightly as Silver spoke, trying to compose himself. "You're right... and I'm sorry." He apologized, wiping his eyes again. "It's just so hard sometimes..."

"I know it is Tails. And it's not wrong to feel sadness." The hedgehog reassured. "But we need you to work right now."

"I understand." The kit nodded with a resigned determination. "I'll have them done tonight, I promise."

Silver patted his shoulder encouragingly. "You're doing well Tails. Just keep it up."

* * *

The technologically gifted fox followed through on his promise, and by the next morning, seven functioning communicators were distributed among the resistance. Silver gave the kit a thumbs up as he strapped the device onto his wrist, and Tails returned it with a small smile.

After attaching his own communicator, Knuckles cleared his threat to gather the group's attention. "We've made the preparations we need for now, and it's about time we focus on the reason we're all here. It's time to fight back against Eggman." The echidna said, shaking his fist. "His robots have left Westopolis, but we don't know where they're headed. Silver, Amy, and Espio, I'm sending you three down to find their trail and figure out what their next target is. Tails and Charmy, you two can continue your scavenging work in the ruins. Vector will help me hold down the fort here for today."

"We'll head down right away." Silver announced with a nod, glancing to Amy and Espio as they nodded affirmatively.

"When you do find the army," directed the echidna, "let us know. And keep a wary eye out for the villains that took down Sonic."

"Understood." The hedgehog replied determinedly, his bracelets beginning to glow as he levitated upwards. Hands stretched out, he lifted Amy and Espio into the air with him, dragging them along as he shot off the island and into the cloudy skies. The cool mists whipped past his face as he soared upward, and soon they were behind him as he floated through the morning atmosphere with his passengers.

 _A clear and unpolluted sky will never get old._ Silver thought to himself with a grin, before turning to check on his little team.

Amy had a wide grin on her face, any sorrows and worries temporarily forgotten about as she enjoyed the feel of flying through the calm air. Espio, on the other hand, had his eyes closed and his face set in a serious expression. His mind was on the task ahead.

Suddenly, the white hedgehog's communicator emitted a high-pitched beep, turning his attention from his passengers to the small device on his wrist.

A press of a button, and the voice of Tails issued from the comm unit. " _Just testing out the communicators. How do you read me?"_

"I read you loud and clear Tails." Responded the hedgehog. "Good work on these things."

 _"They're great!"_ Charmy jumped into the conversation with his uniquely shrill tone. _"I can hear you perfectly!"_

Silver winced at the sound, holding the communicator at a distance. "Yeah, I certainly don't have any trouble hearing you either..." He mumbled to himself.

 _"I'm just glad they work."_ Tails commented in relief, before adding: " _Charmy and I will make our way down to Westopolis later today, as long as the robots are still gone. Let us know what you find down there._ _"_

"For sure, Tails. I'll keep you and Knuckles well updated." The white hedgehog communicated.

 _"Sounds good then. Talk to you later."_

Deactivating the comm, Silver focused his attention on the mission. The mainland was in now view below, and the ruins of Westopolis were plainly visible to the flying trio.

Descending rapidly, Silver hovered low above the rubble and wreckage of the once proud city, setting his passengers down amid the ruins as he glanced around somberly.

While he had never visited this site before, it was still a disturbingly familiar scene to the hedgehog from the future. In his time, nearly every city on the planet rested in this sad state. _I wish I had managed to arrive earlier._ He reflected with regret. _The ruin of the world began here, and I was too late to stop it. I can only hope it's not too late to prevent the rest of the world from ending up like this._

"Silver?" Amy's voice startled him from his thoughts. "Are you alright?" She asked concernedly, as Espio stared at him with a searching expression.

"I... I'm fine Amy." He glanced about the ruins again. "I just hope you all realize that if we lose this war, the whole world will end up like this. Or worse."

"We know it well enough." Intoned Espio. "Let us not waste our time."

Silver nodded, and the group split up to begin their search, keeeping a watchful eye out for any signs of the army that had caused this ruin. It only took a few minutes of searching from the air for Silver to find their trail. Massive footprints in rubble-strewn streets all eventually led to the outskirts of the city, and to a wide trail of pulverized earth that stretched far away over the grassy landscape.

"The army headed north, then." Espio commented.

"They must be heading for Metropolis!" Gasped Amy, alarmed.

"Are you sure?" Silver questioned.

"There aren't any other big cites to the north of here." She responded. "Where else could they be heading?"

"I don't know, I just want to be sure."

"There's only one way to be sure." Interjected the chameleon, gesturing to the path the robots had taken. "Follow them and find out. However, if they _are_ headed to Metropolis, there are a few small villages directly in their path."

"Then let's get moving, and hope we're not too late to help those villages."

Bracelets glowing bright, the hedgehog lifted his companions and himself into the air, shooting off to follow the enemy's trail. It wasn't long before a definite sign of trouble manifested itself. Espio's keen eyes spotted it first - a distant plume of black smoke that rose hazily from beyond the northern horizon.

"Brace yourselves for a fast flight." Silver told his two passengers, as he fixed his eyes on the smoke. The white hedgehog focused his powers, and soon the trio was soaring faster than the speed of sound. The robotic army's trail and the landscape around it became a shapeless blur beneath them, as Silver propelled them over the grassy foothills, straight toward whatever was the source of the smoke plume.

It was - or used to be - some sort of village. But now it was little more than charred rubble. Silver lowered them to the ash-covered ground, as his eyes swept over the smoldering remains, looking for any sign of life or movement. But there was nothing. Not a single survivor was visible, nor were any robots to be seen patrol. The entire area was desolate.

"We were too late." Amy mourned.

Silver shook his head sadly. "We should keep moving. The army's trail continues on, and we need to catch up as fast as possible."

"Wait a moment." Spoke Espio suddenly, his brow furrowed in thought. "Something is not right here." He strode carefully through the streets of the burned village, gazing over the ruins as he spoke: "There are no robotic footprints here. No signs that any robots were in the town at all. And look, the army's trail passes next to the town, but doesn't go through it or change course at all."

Silver raised a curious eyebrow. "They destroyed the town from a distance then?"

"But there are no missile craters, no bullet holes..." Espio rejoined, shaking his head in confusion. "It's as if the town simply burned down, and the robots had nothing to do with it."

"Guys! Come look at this!" Amy called from where she stood at the edge of the army's trail. She pointed to a group of eggpawn footprints that split off from the main path, and headed over the foothills to the east. "Why do you think they split up?"

"I'm not sure." Silver replied. "But if that smaller group is alone, now is the best chance we have to destroy them, before they join back up with the rest of the army."

"One of us should keep following the main force." Asserted Espio. "I can chase them down and keep you aware of their movements, while remaining well-hidden."

The white hedgehog nodded his approval, and the group split up. Espio dashed north along the main army's trail, as Amy and Silver began their hunt for the smaller troop.

Lifting his wrist, Silver spoke into his comm to give Knuckles an update: "Eggman's army is heading north, and we assume they're targeting Metropolis. Espio is on their trail, and Amy and I are on our way to smash a few stragglers."

A moment later, Knuckles replied: _"I understand. If Eggman really is after Metropolis, then we'll have to do our best to defend it._ _Watch your backs, and keep me posted on what you find._ _"_

"We will." The white hedgehog said determinedly.

"Knuckles has really taken to this whole 'commander' thing, hasn't he?" Amy mused as he lowered his wrist, jogging at his side as he set a brisk pace following the robotic footprints.

"Is that surprising?" Silver questioned.

"Well..." the pink hedgehog began. "It's just different, I guess. Knuckles is usually pretty solitary up on that island, so this is a side of him we don't really get to see. I've never known him to be this involved with a problem on the surface."

"It's not just a problem for the surface, it's a problem for him too." Warned Silver. "I know what would have happened - what could still happen, to Knuckles and Angel Island if we don't win this war." His thoughts turned to the letter written by the guardian from his timeline. "Let me just say that it's not a happy ending."

Amy looked down for a moment. "It was really that bad in your future? Sonic never came back? Eggman won completely?"

The male shook his head. "It was worse than you can imagine, Amy. How could Sonic ever come back? Eggman defeated him, and nobody ever heard from him again. I'm sorry, but he's either dead or locked away in a deep dark hole somewhere."

"I refuse to believe he's dead!" The female exclaimed. "Sonic has always come back before, no matter how bad things got! He never gives up, so neither will I." Her eyes were wet with unshed tears, but she blinked them away and continued to keep pace with the white hedgehog.

Silver shook his head, and replied simply: "I admire your faith in him Amy."

The continued on in silence for several minutes, as the midday sun shone down from overhead. A gentle breeze wafted through the air as they walked, and suddenly Silver stopped, his brows furrowed in concentration.

"What is it?" His companion asked.

"Shhh!"

Amy's temper flared for a moment, but she stayed quiet.

Silver paid her no mind, straining his ears to listen. There was a sound, trailing through the wind. It was faint, hardly noticable, but it was definitely there... It almost sounded like...

 _Screaming._

Eyes wide and alert, he grabbed Amy's hand, ignoring her startled protests and dragging her along as he began to race forward.

"What's going on Silver?" She yelled to him as he pulled her onward.

"That!" Replied the white one as they reached the top of the next hill, pointing ahead. Less than a mile away, a small crowd of mobians was being chased by a troop of eggpawns, while a swarm of buzz-bombers circled menacingly overhead.

Finally, the enemy was in sight, and there was not a moment to lose.

"There are only a few dozen bots here, we can take them!" Silver said, golden eyes darting over the scene. Then he paused, turning to the pink hedgehog at his side. "You _do_ know how to fight, right?"

"Of course I know how to fight!" The girl cried, slightly offended. "How is Sonic supposed to appreciate me if I'm not able to fight at his side?" Saying so, she held her right arm out, and suddenly a giant yellow and red mallet popped into existence in her hand.

Silver blinked.

He opened his mouth to question, but the words didn't come.

"Alright then." He finally said, as his bracelets began to glow. "Let's go!"

Adrenaline shot through his veins as he jupped into the air, swooping down the hillside as tendrils of telekinetic energy flowed from his gauntlets. With a swipe of his hand, he sent the closest buzz-bomber spiraling down to the ground, where it crashed in a flaming heap.

Amy was close on his heels, moving much faster than one would expect just by looking at her. A powerful swing of her hammer decapitated an eggpawn, and second swing sent it's headless body crashing into another.

The other robotic minions took note of the newcomers, and shifted their focus away from the terrified mobians they had been chasing. Eggpawns opened fire, only to have their bullets stopped by a telekinetic barrier. Moments later they were knocked to the ground as Silver pushed his hands forward, and before they could even think about righting themselves, Amy had pounded them into scrap metal.

The drone of buzz-bombers was heard close overhead, and laser bursts shot down in rapid flashes. Silver dove out of the way, and his palm stretched out by reflex, sending several of the flying badniks crashing down in flames. Levitating into the air, he stretched out with his power and froze the remaining drones in midair. Amy jumped up, and one-by-one smashed them all to the ground.

Soon it was over, and Silver floated back down to the ground, surrounded by the sparking and shattered remains of the bots. Grinning, he turned to Amy and offered her a high-five. "That was great! Those bots didn't put up much of a fight, did they?"

"Not against us!" The pink hedgehog replied, her hammer disappearing in a puff of smoke.

Silver shook his head again. _I'm going to have to ask her to explain that hammer sometime._

Turning around, he addressed the mobians he had rescued. "Is everybody alright?"

"We're not hurt." A brown cat replied, stepping forward. "Thanks to you."

"Don't mention it." The hedgehog replied, as Amy joined him in front of the crowd. "I'm just glad we made it in time. Are you all from the village directly west of here?"

"We were." The cat replied bitterly. "Until Shadow the Hedgehog showed up last night."

Silver's eyes widened, and Amy's expression grew troubled.

"He showed up out of nowhere late yesterday evening, and before we knew it, everything was on fire. That hedgehog was raging mad, chasing us all out of our homes. It was the scariest sight I've ever seen, like a one-hedgehog army."

"You mean he came alone then?" Asked Silver. "Ahead of the army?"

"What army?" The cat answered, surprised.

"Eggman's army." Silver replied. "If you didn't see it, they must have passed by after Shadow showed up last night." He turned to Amy. "We need to get moving, if we want to catch up to them."

"What about the villagers?" The pink hedgehog questioned.

Silver glanced over the small crowd. "Make your way north to Metropolis. It's where Eggman's army is headed, but for now it's the safest place nearby for you to stay. We'll be there soon as well, and we'll defend the city as long as we can."

The villagers murmured amongst themselves for a moment, before starting to walk away toward what they hoped would be safety. The brown cat lingered a moment, offering a simple "Thank you." for defeating the robots. Then he too was on his way to Metropolis.

Silver watched them leave, then raised his communicator. "Espio, can you hear me?"

 _"Yes."_ Came the terse reply.

"We just finished trashing those bots we went after. We rescued the citizens of that destroyed village, and they told us that Shadow is the one responsible. Stay alert and keep an eye out for him."

 _"Understood."_ The chameleon replied. _"You should know that I've passed two more villages, destroyed just like the first one. Their citizens are probably in the same predicament as the ones you just rescued."_

"I see. We'll do our best to find them. Until then, let us know when you catch that army."

Deactivating his comm, Silver shook his head. A mental push sent both him and Amy into the air, and flying off to the north. Turning to the pink hedgehog, he exclaimed: "This doesn't make any sense! Why would Eggman send Shadow ahead to destroy these towns and scare away their citizens, only to split up his army later by sending parts of it after the civilians Shadow scared away earlier? Why not just deal with the citizens the first time?"

"None of this makes sense, Silver." Replied Amy with a shake of her head. "The Shadow I knew wouldn't be working for Eggman at all. I don't understand what happened to him!"

"What do you mean he wouldn't be working for Eggman?" The white hedgehog asked curiously as they drifted through the air. "I haven't heard much about Shadow, but none of it seems good."

Amy looked down at the ground passing beneath them. "Shadow isn't a bad guy." She said finally. "At least, he wasn't before. Did nobody tell you about Maria?"

* * *

Several long minutes of storytelling later, Silver felt that maybe his life wasn't so bad, considering what Shadow had gone through.

"I was there, you know." Amy finished sadly. "I helped remind him of Maria's wish, and I was there when he finally remembered it all. If you saw him then, like I did, you'd _know_ that Shadow isn't a bad person."

"Then how do you explain all this?" Silver asked confusedly. "He beat up Tails, he helped defeat Sonic, he burned down these villages..."

"I can't." The girl replied, shaking her head. "I just know that it doesn't make sense."

Silver turned away from her, staring instead at the horizon he was flying them towards. _She isn't wrong._ He thought to himself. _Something is very odd about all of this._

Any further thoughts on the matter were interrupted as another troop of robots came into view ahead. But this time, the evil minions had already caught their prey. In front of them marched a large group of captured and restrained mobians, their heads bowed in defeat. Dropping to the ground, Silver glanced over the enemies as Amy's hammer materialized in her hands again.

"There are more robots than last time, but they shouldn't be a problem." He spoke. "We just need to make sure those civilians don't get caught in the crossfire."

Suddenly, there was a flash of light behind the robots, who immediately turned to face whatever had caused it. Immediately an explosion rang out, followed quickly by a hail of gunfire, kicking clouds of dirt and smoke into the air.

Acting on instinct, Silver launched himself toward the scene, positioning himself protectively between the terrified mobians and their metal captors. The robots seemed to have completely forgotten about their prisoners however, as something blew them apart one by one. The smoke and dust kicked up by the battle quickly obscured the scene, and the hedgehog couldn't discern what was happening. Flashes of light illuminated the debris cloud for brief instants, while sounds of explosions and crashing metal were heard from within. Then, as fast as it had begun, it was over. The dust began to clear, and Silver readied himself for whatever was coming, arms raised and prepared for a fight.

But nothing happened. The afternoon breeze slowly carried the smoke away, and revealed only the shattered and scorched bodies of several dozen eggpawns. Amy was wandering among the wreckage, and she turned to Silver with wide eyes, speaking in a low voice:

"Shadow was here."

* * *

Several miles away, a flash of chaos energy deposited a red and black figure at the top of one of the area's largest hills. The Ultimate Lifeform stood with crossed arms and a stoic expression, absorbed in silent thought as his keen eyes surveyed the landscape below. He had not expected to run into Amy Rose, of all beings, as he fought to save the mobians he had run out of their homes the previous night. And who was the white hedgehog helping her?

Shadow shook his head. _It doesn't matter._ He decided. _I'm not going to get involved with them. Not while Infinite is still flying around using my form to commit his crimes._

He hadn't seen the masked jackal since last night's brief encounter, and for the moment Infinite no longer appeared to be leading the robotic army. Where he was, Shadow couldn't begin to guess. But if he stayed away, then perhaps the Doctor's army could be defeated in battle once they reached Metropolis. The odds weren't great, but they were good enough for the dark hedgehog.

His next course of action decided, the hover-skates on his feet activated with a quiet whine, and the dark figured raced away to the north.

* * *

Meanwhile, Silver and Amy had contacted Knuckles and Tails. The mobian prisoners, citizens of both remaining destroyed towns, had been released from their shackles and sent onward toward Metropolis. Then, the two hedgehogs tried to explain the situation to their comrades.

"Amy is convinced she saw Shadow destroy the bots." Spoke the telekinetic hedgehog. "I couldn't tell who or what it was, only that they worked fast. But if it was Shadow, that raises a lot of questions."

"How could it be Shadow?" Knuckles grunted through the comm. "He's working for Eggman, Tails and those villagers can attest to that!"

"Maybe Tails misunderstood what he saw?" Defended Amy. "Maybe it was another of Eggman's shadow androids?"

"I know what I saw and felt." Came Tails' slightly bitter voice. "I have nightmares of it. The look on his face as he attacked Sonic and I... That's not something an android can replicate."

"I know what I saw too!" Cried the pink hedgehog. "Shadow was the one destroying those bots, to free the villagers!"

"You mean the villagers whose towns he burned down less than 24 hours ago?" Rejoined the fox.

"Enough!" Yelled their commander. "This is getting us nowhere."

Silence reigned for a moment, as Amy's head drooped, and Silver shook his head.

"Knuckles is right." The white hedgehog agreed. "Espio is on the heels of Eggman's army, Metropolis is in grave danger, and we're all standing here arguing! Whatever is going on with Shadow, we'll find out eventually. Until then, there's a city that needs our help, and an army of robots that needs to be smashed."

"Exactly, Silver." Continued Knuckles. "Now I want you and Amy to head straight to Metropolis. Espio can meet up with you once the army arrives. Tails will join you tomorrow. We have a big battle ahead, and we need to be ready for it."

"Understood commander." Answered the white hedgehog, lowering his wrist. A few moments later, he and Amy were levitating rapidly through the air toward Matropolis, and the coming battle.

The sun was low in the sky now, as afternoon stretched into evening, and Silver pushed himself faster. Questions floated continuously through his mind without answer. _Are we ready for the battle ahead? Are a few fighters enough to hold back an entire army? Will the masked stranger show up here? And what part does Shadow play in all of this?_

The answers, pleasant or not, would come soon enough. With determination settling over his face, the white hedgehog stared ahead, and steeled himself for what was to come.

* * *

 **Author's Note:**

 **Ok, that was the longest single chapter for this story so far - not even close. Sorry if it seems a little dry at times, but this chapter is important to set up some things later. I also felt the need to get some real interaction between these characters, something that the games never seem to do these days. We've seldom seen characters grow and be taken seriously since the adventure days. (And 06, but let's not get into that mess.)** **In this story, I want to really develop them. They're all still dealing with what's happened to Sonic, and the mystery surrounding the villains, and still trying to figure out this whole resistance thing as well, so I wanted to showcase some of that as best I could. Hopefully it turned out well.**

 **Anyway, I hope you all enjoyed this chapter, and I'll try to get the next one out quicker for you.**

 **As always, reviews, questions, and opinions are welcome and appreciated. See you next time!**


	12. The Siege of Metropolis - Pt I

**Author's Note: Again, sorry for the long delays between updates. I want to get at least one chapter out every week, but life conspires against me. :/**

 **Many thanks as usual to my wonderful reviewers.**

 **bajy \- Thanks!**

 **Infinite's Ruby \- This story is as much about character interaction as it is about fighting over the fate of the world, so I'm pleased that you think it's been done well so far. Especially Amy - I really want to take her seriously in this story, without drastically changing her character. She'll be an important player in this story, unlike in Forces.**

 **MobiusHero \- Short answer or long answer? :) Short answer: Parts of the game, a lot of additional stuff. Long answer: The main point about the Forces plot, is that there's basically nothing to it. What little story we do see is full of plot-holes and bookends a giant 6-month void that I get to fill with whatever I want. So while I'm keeping several main points from the game plot (Infinite's origin for the most part, Sonic gone for 6 months, virtual reality enemies, etc.), you're also going to see a lot of new things and improvements that weren't in the game. For example, Espio mentions Seaside Hill at one point. But instead of letting us go there in the game, we get Green Hill again. And again. And again. (I truly love the game, but come on, SEGA.) So, ****you're definitely going to see at least several locations from other games here.** **You're also going to see more than 5 seconds of Chaos here. And more than 3 minutes of Metal Sonic. And as for a full our war between the armies - absolutely. You see hints of those big battles in the level backgrounds for the game, and it looks really cool, but you never see any of it up close. So I want to explore that a bit. Anyway, sorry for the rant, but I wanted to get a detailed explanation out here for you.**

 **PetsnanaG \- I'm happy you liked it! _Cruel Work_ was one of the most interesting chapters for me to write, and I wasn't really sure how well it would turn out, so I'm quite pleased to have seen such a positive reception.**

 **mooninescent \- Those three will have a lot more interaction, especially in the later chapters, I can promise you that. I hope you enjoy it even more as the story goes on.**

 **Awdures \- I'm glad you enjoyed it!**

 **TheLastoftheRealOnes \- You're quite welcome. Shadow is always a fun character to write, so you'll see more of him pretty soon.**

 **And now, here's chapter 11 for you folks. There's a lot of action in here, so hold on tight!**

* * *

Chapter 11 - The Siege of Metropolis - Part I

* * *

Metropolis. By far one of the largest and most prosperous cities on the planet. It's population was largely mobian, amounting to over 3 million souls, and it's boundaries stretched out to encompass an area of more than 200 miles squared. It was the world's major hub of technology and innovation, and the expansive skyline reflected that fact. Gleaming white towers of nearly every shape and size imaginable, were all clustered together in a tightly packed urban jungle. Highways and viaducts weaved and curved their way through the cityscape, flowing with traffic like the veins and arteries of some great living organism. Billboards and jumbotrons littered the sides of buildings and the plazas below, flashing with colorful advertisements or the latest trends. At night, the excessively well-lit city shone as bright and reflective as any precious jewel, standing tall and proud as a gleaming and awe-inspiring monument to civilization itself.

But now a grave threat faced the mighty Metropolis, as a massive army of metal war machines gathered, less than a dozen miles outside the city limits. The normal hustle and bustle of life in the city was replaced with the awful terror of war. Panic reigned supreme, as the population faced he loss of all their wealth and success, and quite possibly their lives as well. Lawless rioters and panicked evacuees thronged together on the streets, in a massive demonstration of civil unrest. The hero they had relied on for so long to protect them was now gone, and no hope was in sight.

In the midst of all this confusion and hysteria, two tired yet determined hedgehogs slipped into the city one night, almost completely unnoticed. They were soon joined by a stealthy purple chameleon, who had spent a full day of chasing and tracking the evil army that now threatened the city. And hundreds of miles away at the same moment, a floating island was slipping unseen through the clouds, carrying its passengers directly toward the scene of the brewing battle.

Eggman's army would not march into Metropolis unopposed - The Resistance would be there to stand in the way.

* * *

Deep in the ornate caverns that wound through the heart of Angel Island, Knuckles the Echidna stood over the Master Emerald, his hands stretched out and his eyes closed in concentration. His connection with the Master Emerald was strong, and he used his influence over the gem to steer the floating landmass northward. The island responded to the power that kept it afloat, and sailed onward through the cloudy night skies. After a moment, the guardian stepped back with a sigh, satisfied that the island was in it's proper course, and stood gazing for a moment at the magnificent gem. It glowed brightly in the dark cavern as it's eerie light reflected off the numerous murals and polished stones that decorated the walls. With his arms crossed and his face expressionless, Knuckles drifted off into thought as he stared at the centerpiece of his existence.

It wasn't without some trepidation that he was steering the island and it's treasure directly toward an active war zone. It made him uncomfortable to have the emerald so close to the powerful forces of the only man to have ever stolen it. It went against his natural instincts as a guardian. In the past, he would have done everything in his power to keep Angel Island _away_ from controversy on the surface. But things time and experience had changed him. Surface troubles could reach into the skies, and nothing illustrated that better than having a giant space station, a mad doctor, and a hyper-active hedgehog all suddenly crash on the island.

Eggman and Sonic had taught him much. Eggman had taught him a painful lesson about trusting strangers, a lesson which was only reinforced through interactions later years. And Sonic... He had taught him about life apart from the emerald. Through controversy after controversy, adventure after adventure, Sonic had forced him to interact with the surface world, and to play a part in solving it's problems. The hedgehog had also taught him about friendship, teamwork, and about never giving up. Yes, the guardian knew he wasn't the same echidna he had been all those years ago. The Knuckles of today was steering his island _toward_ the danger, because he knew he couldn't sit this out. Sonic was gone, and the world below desperately needed help. If there had been any lingering doubts, Silver's document had settled the matter nicely. Staying out of this war would not end well.

So, with a final glance at the shimmering emerald, Knuckels turned and headed up the ancient stairway to the surface.

As he stepped out of the hidden door in the emerald altar, into the cool and quiet night air, he was met by Tails, who had been standing there waiting for him.

"I just thought I'd let you know." The fox began. "Silver, Amy, and Espio are all in Metropolis now, and Eggman's army is gathering outside the city. Silver said the population is already caught up in complete panic and unrest."

Knuckles grunted. "That's not gonna make our job any easier. Did they see any more of Shadow or the other villains?"

"No." Answered the kit. "Espio didn't even see any of them among the army, and he got pretty close from what I understand."

The echidna nodded, thinking. "We'll have to keep an eye out, but if we're lucky, Eggman doesn't expect much resistance now that Sonic isn't here. The best advantage we have is that he doesn't know we're coming."

"Right." Agreed Tails. "So what's the plan for tomorrow?"

"We should reach Metropolis by early tomorrow morning. I'll try to find the island some cloud cover, otherwise I don't want to get very close to Eggman's forces. You, Vector, and Charmy will head down to the surface as soon as possible, and together with Silver's group, organize to fight back however you can."

"You're not coming?" The kit questioned.

"Not with the emerald this close to danger." The guardian spoke firmly. "I'll stay as close as I can, in case you guys need to get out of there. But if Eggman finds out that I'm involved in this, Angel Island becomes a big target, if its not already. I have to protect it for as long as I can. For the sake of the emerald, and for the resistance as well."

Tails nodded in understanding. "Alright. We'll do our best without you then."

Knuckles patted the young fox's back encouragingly. "I know you will. Now let's get some sleep. We'll all be needing it tomorrow."

* * *

The night passed quickly, and soon the time of departure was at hand. The pre-dawn skies were obscured by a fortunate cloud layer, and Knuckles carefully maneuvered the island to stay concealed inside of it. Meanwhile, Tails, Charmy, and Vector stood ready at the edge of the floating landmass, preparing for the trip to the surface. Charmy was perched on the ledge, anxious as ever to get going, and Tails stood determinedly beside him with a bag of improvised weapons slung over his shoulder. Vector stood a few steps behind them, speaking into his communicator.

"We're about to head down Knuckles." The crocodile reported briefly, as the trio stared out into the cloudy void.

From the emerald chamber in Hidden Palace, the guardian responded soberly: _"Good luck you guys. Watch each other's backs out there, and give Eggman my regards."_

"You can count on it." The crocodile said with a grin. Then he turned to his partners with a simple: "Let's do this!"

Charmy and Tails each grabbed one of Vector's hands as the trio stepped off the island's edge, and together they carried the heavy croc as they descended rapidly through the clouds. But soon enough the mists gave way, and clear air revealed the outskirts of Metropolis less than a mile away, shining brilliantly in the early morning light. Eggman's army stood off to the west, a giant mass of metallic war machines, of every shape and size. They stood rigidly in tight formations, completely prepared for battle, but not moving an inch yet.

"What do you suppose they're waiting for?" Charmy asked as they approached the surface.

"A signal from Eggman perhaps?" Pondered Tails. "Or maybe the arrival of Shadow or that masked stranger."

"Either way," Vector pointed out as they landed, "it won't be good news when they do start moving. Let's hurry!"

* * *

Meanwhile, Silver stood silently on the observation deck of one of the highest towers in the city, looking out at the jungle of glimmering buildings below, and then to the menacing enemy forces amassed on the horizon beyond.

The hedgehog from the future knew exactly what would eventually happen to this prosperous urban utopia if Eggman won the war. He hadn't made the connection before, but as he stood here now and looked out over the landscape, he found that he recognized the hills and mountains in the distance. This massive city still stood in the ruined future - but only because Eggman made it his capital, and had rebuilt it in his image. If his empire won, Metropolis would be remade into a lifeless conglomeration of industrial complexes, spewing toxins into the sky and pumping out more minions for the evil doctor to rule over. In Silver's time, this once peaceful and shining city was a dark and fearful place that symbolized the might and power of the evil empire that ruled over it. Even the name Metropolis was itself lost to history, as the empire rebranded it's capital with a far more fitting title - Robotropolis.

 _So much is at stake._ Worried the white hedgehog, as he stared out at the massive army of war machines. _We can't lose this. We just can't._

Further thoughts were interrupted by the sound of a door slamming open behind him, as Amy stepped out to join him with an angry frown on her face.

"I went to talk to the mayor." The pink hedgehog announced sourly.

"...And?"

"And the coward already fled the city." She replied, fists clenched angrily. "All those people in danger and in a panic down there," she cried, gesturing at the tempestuous crowds below, "and their mayor just flees without any thought of helping them escape or fight back! How could he do that?"

Silver shook his head with a sigh. "Fear can make people do awful things, Amy. Some people will do anything to try and save themselves, even if it means abandoning others who are in the same danger."

"I just don't understand how anybody could do such a thing and live with themselves afterwards." The girl ranted, slamming her fist down on the railing. "So many people are in danger, everybody should at least be _trying_ to help them!"

"Some people just aren't as brave as you are, Amy." He replied sadly, before turning to her with a questioning glance. "What gives you the courage to wade into a war like this?"

Amy was silent for a moment, before answering softly. "I suppose it's because of Sonic really... It's what he would do." She bowed her head, then continued in a tone full of melancholy: "He would never abandon a single person who was in need of help, no matter how bad things got. He inspires me to be brave like that... To help people who need it, even when I'm afraid."

Silver nodded slowly as the girl spoke, patting her hand as she finished. "I think Sonic would be proud of you right now. It's not an easy thing to face down an army like this, but here you are. I think he'd be very proud."

The pink hedgehog's eyes watered, and she wiped them clean with a small smile. "Thank you Silver." She whispered. "That means a lot to me."

The white hedgehog smiled, then turned back to the railing. In a moment, his smile had faded, and was replaced with a serious frown.

"We've got trouble." He announced, pointing a gloved finger at the horizon. "There's why Eggman's army was waiting so long to attack."

Amy followed his gaze, and her eyes widened. "Oh..."

There, low above the distant western horizon, was a massive fleet of airships. Some were far larger than others, but all of them shared the same basic design profile, red and yellow color scheme, and the black insignia of the Eggman Empire emblazoned on their sides. Dozens of them, or perhaps hundreds, floated together through the morning skies in widespread formations, positioning themselves above the force of robots spread out on the surface below. Together, they formed a fearsome and formidable army that glinted sharply in the sunlight as it began a firm march toward Metropolis.

"The Egg Fleet." Muttered Amy, as she watched the approaching enemy with wide eyes.

"We need to get moving." Silver said determinedly, his bracelets beginning to glow. " _Now_."

As he levitated himself and Amy through the air, an urgent voice issued from his communicator: _"We've almost reached the city!"_ Announced Tails. _"I assume you're all seeing the same thing we are out here?"_

"We see it Tails." He replied, weaving his way between skyscrapers. "Meet us at the western edge of the city, and hurry!"

Only a few short moments later, the Resistance was gathered together on the outskirts of Metropolis, standing as the only barrier between the approaching army and the massive city behind them.

Terse greetings were exchanged, and then Tails spoke up, lifting the heavy sack he had brought from Angel Island. "I salvaged these from eggpawn blasters, and rigged them for use as personal weapons. If there's anybody in the city willing to fight, we can hand these out to them. It's not much, but it's better than nothing."

Silver nodded. "Charmy, take these weapons and hand them out to anybody willing to fight for the city. We'll need all the help we can get."

"Everybody else, do whatever you can to stop these robots." He directed firmly. "Eggman wants this city more or less intact, for use as his capital. I know, because in my time that's what this place is - Robotropolis, capital of the empire. We can't let that happen here and now." He glanced around at the small but determined group. "Do whatever it takes. Eggman won't completely flatten the city like he did Westopolis, so draw the robots into the buildings and the streets, use them for cover as you fight."

Raising his communicator, he contacted Knuckles. "The robots are marching on the city as we speak, and they've got a fleet of airships backing them up. Wish us luck commander."

 _"Stay safe out there you guys."_ Came the solemn response. _"I'm keeping close by in case you need to retreat in a hurry."_

Silver shook his head, determined not to let it come to that.

"Alright." He announced, as the enemy drew ever closer. "It's time to show Eggman what he's up against. It's time to make him pay."

"For Sonic!" Cried Tails, fist raised defiantly in the air.

"For Sonic!" Repeated Amy, her hammer materializing in her hands.

"For Westopolis." Voiced Espio, to agreeing cheers from his teammates.

"For the future!" Shouted Silver, his bracelets and palms glowing bright and vivid.

Not a moment later, the first cannon blasts from the Egg Fleet struck the ground in front of them, and the battle began.

Charmy immediately zipped back into the city to distubute Tails' bag of weapons, and the other five Resistance members braced themselves defensively as the ground beneath them shook under the Egg Fleet's barrage. Dirt and debris was thrown into the air, and a battalion of eggpawns swarmed quickly forward through the dust clouds.

Silver took a deep breath as adrenaline shot through him, and his battle instincts took over. The first wave of Eggpawns had barely caught sight of him before they were knocked onto their backs by a psychokinetic wave, and quickly smashed into scrap metal by Vector and Amy. Tails darted forward a split second later, curled into a tight spin-dash that ripped straight through the robotic minions in his path. Running forward, Silver ducked below a laser blast, flinging a glowing hand out toward the bot that had fired it. The metal body crumpled beneath the psychic blow, and the white hedgehog sent it's remains flying with deadly force at the next several enemies. Espio appeared out of nowhere nearby, vanishing a moment later as three robots ahead fell to the ground with shuriken stars embedded in their metal skulls.

Giant footsteps shook the battlefield, and Silver turned to face a giant metal behemoth stomping it's way forward. Launching himself into the air, the white hedgehog dodged around the massive spiked fist sent his way, and landed on the metal monstrosity's head. Placing his hands on the armored metal surface, the cyan glow around the hedgehog intensified as he focused his power, ripping the giant's head from it's shoulders with a yell, and sending it crashing down onto a group of eggpawns below. Levitating up again, Silver watched as the behemoth's headless body teetered precariously, then at last fell to the ground with an earth-trembling thud.

 _One down, several dozen to go._ The white hedgehog thought grimly, turning to face the next wave of the onslaught.

* * *

Back on Angel Island, Knuckles wordlessly paced the floor of the emerald chamber.

As guardian, his duty was to the gemstone beside him. But as leader of the Resistance, his mind was wholly occupied with thoughts of the ongoing conflict below. Seldom in his life had he felt more conflicted. He itched to be on the ground with his friends and allies, smashing Eggman's mechs and letting out some of his anger. But to leave the island and the emerald alone now, this close to danger, would just be begging for trouble.

It had been his own idea to remain behind, and he knew it had been the right decision. But he still couldn't help the frustration he felt, unable to do anything but sit alone and hide his island in the clouds, while on the surface others were fighting and perhaps dying to keep Eggman's armies out of Metropolis.

Sighing in resigned frustration, the echidna sat down beside the emerald and lifted his communicator.

* * *

 _"How are things going down there?"_

Ignoring the voice from his comm unit, Tails hit the ground harshly as an explosive shell from one of Eggman's airships impacted the street in front of him, filling the air with dust and debris. Coughing, he got back to his feet and lifted his wrist, speaking wearily: "Not very good, Knuckles." A laser blast narrowly missed his foot, and the fox turned to charge at the nearest eggpawn, ripping through it's thin armor with a quick spin-dash.

"Poorly built tin cans." He muttered under his breath, as he ripped the arm off another pawn and jammed it into the robot's neck joint. The bot spasmed and collapsed, and Tails took a brief instant to catch his breath, before raising his communicator again.

"They've forced us back into the city already, and most of us are separated from each other." He reported tiredly. "I don't know how much longer we can keep this up, there's just _too many_ of them."

Shards of glass and metal showered the street as another shell impacted one of the nearby buildings, and Tails dove for cover. "Especially with that egg fleet sitting up there and using us for target practice!"

An airship's turret flashed, and yet another shell screamed through the air toward the fox, as he jumped into the air to dodge it. But there was no need. A pulse of teal energy slammed into the shell, detonating it in midair, and Silver floated down in a cyan glow from above, breathing heavily.

"You good?" The white hedgehog asked.

The fox nodded quickly, and together they ran for cover from the airship's line of fire.

 _"Tails?"_ Came the worried voice of Knuckles from the communicator.

"I'm fine." The kit replied. "But we need to do something about those airships, or we're not going to last very long at all."

"I'd fly up there to take them on myself," interjected Silver "but they're flying so high that I'd be an easy target on my way up."

"There are just too many enemies for us to take on at once, and we haven't even seen Shadow, the masked guy, or the other major players yet." Tails warned.

 _"Then maybe we need to fall back while we still can."_ Suggested Knuckles.

Silver was about to make a reply when he was interrupted by another voice from the communicator.

 _"We're pinned down with a group of injured civilians."_ Espio informed urgently. _"We need immediate assistance!"_

The hedgehog was in the air an instant later, with Tails on his heels, homing in on Espio's comm signal.

"We're on our way!" Yelled Tails as they flew. "Hang on!"

"We can't retreat, and this is exactly why." Silver announced firmly. "There are people here who need our help."

 _"Then evacuate the city before you retreat."_ Knuckles spoke. _"It's clear that we're not going to win this battle outright."_

"Evacuate more than 3 million people?" Cried Tails. "To where? The robots have already breached the city, there's no time for that Knuckles!"

The echidna went silent at that, apparently out of ideas.

Finally they reached Espio, who was battling alongside his teammates and a few armed citizens to protect a huddled group of mobians in the middle of an open plaza. Descending rapidly, Silver and Tails joined the Chaotix in the fray.

"How bad are their injuries?" Silver questioned as he knocked a wave of eggpawns back.

"A few broken limbs among the worst." Answered Espio. "Several likely concussions. Nothing that would prevent them from being moved, if we can find a way."

"Keep the bots occupied over there!" Shouted Tails. "Charmy and I will take care of the injured!"

At that moment, several airships opened fire on the group. Silver raised his arms in a desperate attempt to shield them, bracelets shining brightly as he creating a psychic barrier that deflected the incoming projectiles.

"I can't keep this up long!" The white hedgehog groaned aloud as more shells impacted, straining to maintain the shield. His companions braced themselves, preparing to drag the injured mobians along and run for their lives once the barrier collapsed.

Then, just as Silver was about to give up, the barrage ceased. The resistance members looked up in disbelief as the Egg Fleet slowly reoriented itself. The turrets that had just previously been firing on them now suddenly began to rotate away.

"What's going on?" Vector wondered aloud, voicing the thoughts of the entire group.

Suddenly, a group of blue and grey jet aircraft roared overhead at high speed, banking toward the egg fleet. Each wing was emblazoned with a white letter on a circular red and blue background.

"It's GUN!" Cried Tails.

The group gave a loud cheer as the planes fired a series of missiles toward Eggman's lead airship, and bright explosions blossomed upon their impacts. More GUN aircraft appeared, while the Egg Fleet deployed its own defenses, and soon the sky above was embroiled in a massive battle.

The sound of whirring blades filled the air, and a large transport helicopter appeared over their heads, landing nearby a moment later. It's door slid open, and several medics rushed out toward the injured mobians.

As the resistance members watched the unexpected arrivals with shock and relief plain on their faces, Rouge the Bat emerged from the helicopter, with one hand on her hip and a wide smirk on her face.

"It looks like you boys could use a hand."

* * *

 **Author's note: To be continued!**

 **As I've mentioned before, GUN is going to play an important role in this story. They're a big player on the world stage, and since Eggman is trying to take over the whole world here, it only makes sense that they'd be involved one way or another. You'll see _how_ involved they get over the next several chapters. ****Also, yes, I know that GUN wasn't in the game story. No humans at all (besides Eggman) were in the game story. But I included humans in this story, largely because Shadow was in this story, and without humans Shadow doesn't have an origin story. Soooooo...**

* * *

 **I hope you all enjoyed this chapter, and please don't hesitate to ask any questions or offer your opinions on this story. We're still barely past the beginning, with a long way to go, so I hope you'll all stay with this story until the end!**


	13. The Siege of Metropolis - Pt II

**AN - Alright, late night update!**

 **Thanks as always to my reviewers - you don't know how much I appreciate them.**

 **PetsnanaG \- You wanted to see how they'd get involved, read this chapter and let me know what you think! This is only the beginning. :)**

 **TheLastoftheRealOnes \- If that was your reaction, then I've succeeded at my goal in writing this story. :) I think Rouge is one of the funnest characters to write sometimes, partly because she has such interesting and complicated relationships with people like Knuckles and Shadow. And yeah, people tend to overlook her character too often in favor of her... shall we say, _other attributes_.**

 **Alexandria Prime \- And get involved they will, as you'll see. It really bothered me in the game story that GUN was just ignored while Eggman took over the world. Well, _everything_ was ignored, but you get my point. **

**endless-pastability \- Wow. First off, let me just say thanks. The fact that my story was so good in your eyes, you created an account just to review it? That means a lot to me. Secondly, doing the characters justice is the biggest reason I decided to write this fic in the first place. So many of these characters have such potential, or such depth to them, they could be amazing stories if done right. I want to have a lot of character interaction a development in here, while at the same time remaining faithful to who they are at their core. Sadly, most people (SEGA included) just don't take them that seriously. And yes, Sonic after his torture is going to be the most important part of this story to me. How do you put Sonic through all that, and yet see him come through it all in the end? How does he change, how does he stay the same, how does it impact others? _That_ is what I want to see in a story, and that's what I'm going to do here.**

 **MobiusHero \- Yeah, the plot is definitely kicking in now. And don't worry, answering review questions is the easiest part of writing this story, so ask me as much as you want, lol. The phantom ruby was and is one of the hardest things about this story. In the game, Shadow says Infinite's replicas are "as formidable as the originals". But then, half an hour later, a bunch of OCs fight off an army of Shadow, Metal, and Chaos clones by shooting _lasers_ at them. (Were you even trying, SEGA?) Anyway, the phantom ruby (if you take it seriously like I do) is _insanely_ overpowered. So, I've put a few limitations on it in this story. I don't want to spoil them all here, but I *will* point out that Shadow escaped Infinite in chapter 6 by using chaos powers. The short answer is, virtual reality villains will be a _very_ big threat, until the secret to defeating them is discovered. As for the second question, there will be a resistance army eventually, and we'll get to see the big battles that happened in the game backgrounds, but were never shown up close. There will be serious fighting, and all that comes with that, but I am probably going to gloss over some of the more gory details, because I don't want this to be an M-rated fic. As for character death, this story is modeled (however loosely at this point) after Sonic Forces the game, so the end result will be much the same - all the familiar faces living on, able to head off into the next adventure. — ****Or the next story I write... (I'm nowhere near done with this story, and I've already got a sequel in mind. Someone help me. O_O)**

 **Awdures \- I'm glad you liked that Knuckles part, I've always felt that we need to see more of his struggle between his guardian duty and his duty to his friends. (SEGA of course just ignores the emerald these days.)**

 **Infinite's Ruby , bajy, and Extreme Light 9 \- Thanks! I'm glad you're enjoying the story, and here's the next chapter for you all!**

 **Without further delay...**

* * *

Chapter 12 - The Siege of Metropolis - Part II

* * *

Heart-tipped boots stepped out of the helicopter, as teal-green eyes swept over the surprised faces of the resistance members. Rouge the Bat wore a proud smirk on her face, as GUN fighters swarmed the skies overhead in close combat with the Egg Fleet, giving new hope for victory in the battle for Metropolis. But behind her smirk, the skilled female agent's mind was at work, taking note of the dirty and haggard faces before her.

Each of those faces was covered in soot and oil, while minor bruises and scrapes decorated their bodies. Amy, Vector, and Charmy were busy helping GUN medics attend to the injured mobians, while Espio tended to a small cut on his left arm. Silver was holding a hand to his forehead, mentally strained after the effort of shielding his companion. Tails, despite being as bruised and dirty as the rest of the group, was at least well enough to smile at her arrival.

Shaking off his surprise, the fox rushed forward to greet her. "Rouge!" He cried excitedly. "You have _no_ idea how happy we are to see you."

Once again sweeping her trained gaze over the little group, the batgirl turned to Tails with a wry grin. "I think I could hazard a guess, foxboy."

The kit grinned sheepishly, as Rouge continued to speak. "But enough with the small talk. If you're all still in once piece, then its time to get down to business. The good Doctor didn't expect to see GUN here, and we've got him off balance. Let's make the most of it."

Tails nodded, glancing up at the chaotic battle above the city. "With the Egg Fleet occupied, it shouldn't be too hard for us to fight off the ground forces. The only problem is they're so spread out now, trying to get around us and into the heart of the city."

"Well that shouldn't be _too_ big of a problem." The agent said with another smirk. "I have several divisions of Rhino tanks at my disposal. We can send them through the city to clear out the stragglers, while we push back against the main army."

"That could work." Mused the fox, his mind quickly working through the strategy. "If GUN keeps the airships and stragglers taken care of, we just might be able to win this. I only hope we don't run into Shadow here - Silver and Amy say that he's been in the area."

A troubled look passed over Rouge's face at the mention of the black hedgehog, but it was gone a moment later. "We'll have to cross that bridge when we get there. For now, let's get to cracking some Eggman."

* * *

Far across the battlefield, several miles behind the massive robotic army, a lone figure stared with piercing gaze at the conflict spread out before him. His crimson eyes darted to and fro, watching as explosions lit up the skies over Metropolis, and smoke billowed up from the besieged city's outskirts. With arms folded tightly across his chest, and feet planted firmly on the grassy earth beneath him, Shadow the Hedgehog contemplated his next move.

His original plan had been to simply charge into battle and rip apart anything in his path. Infinite was curiously absent, and the robots would be spread out as they swarmed into the city, presenting a very favorable opportunity for the Ultimate Lifeform to unleash his wrath on them.

Unfortunately, as with everything in his life, fate wouldn't let it be so simple. For starters, the black hedgehog had just yesterday stumbled across Amy Rose and another unknown hedgehog, leading him to assume that Sonic's friends hadn't given up the fight yet, and were probably gathering to help defend Metropolis. Normally, that wouldn't be of much concern to him. But thanks to Infinite's trickery, Sonic's friends doubtless viewed him as a traitor and an enemy, and likely wouldn't hesitate to attack him. Then, as if the lone hedgehog didn't have enough to deal with, an armada of GUN forces had suddenly shown up out of nowhere, swarming through the skies and streets of the city. And even though they were here to fight against Eggman, that militaristic organization had never taken kindly to traitors. They likely had a death warrant out for him already.

But despite it all, Shadow just couldn't turn away from the fight. It wasn't in his nature to back down from a challenge, especially with the fate of millions at stake. It didn't matter if the entire world wanted him dead - Shadow would still fight to protect it, as he had promised.

Clenching his fists and activating his hover-skates, the black hedgehog braced himself for battle, feeling the power of his chaos emerald flowing through him. With eyes blazing and face set in a determined glare, Shadow charged forward, approaching the robot horde from the rear. He was quick as lightning, and _far_ more deadly. The first troop of eggpawns were lucky to get a fleeting glimpse of black and red before, being ripped apart by a dark blur, and a flash of chaos power. Adrenaline and battle instinct took over, and the black hedgehog was nothing but a rush of wind amid the legions of his enemies, leaving a trail of complete destruction behind him.

No matter how much the world around him changed, no matter how many allies he lost, no matter how many people wanted him dead - Shadow would fight. And that fight would never change. It was familiar, in a way. He had been born into this carnage - combat was his nature, destruction was his element. And as the black hedgehog found himself in the chaotic rush of battle, a feral grin worked its way onto his face.

* * *

Cyan energy flashed, and several eggpawns fell to the ground in pieces. Golden irises darted to the side, and another flash knocked a group of buzz-bombers out of the sky. Silver raised a glowing hand, lifting the metal corpses, then turning and hurling them against the next wave of enemies. A swarm of GUN drones flew overhead, harassing the enemy from above, and the white hedgehog pressed forward. It wasn't easy for him to constantly use his powers to such an extent, but fierce will and determination kept him fighting.

Brilliant explosions lit the sky above, as several missiles struck their target, and one of Eggman's airships broke apart in midair, hurtling to the ground in flaming pieces. Silver leapt to the side, dodging the falling debris and landing next to another group of eggpawns. On instinct his hands went up, and he froze them in their places. But before he could finish taking care of them, an orange blur dropped from above and slammed into the bots, quickly knocking them to pieces. Tails unfurled from his spin-dash a second later, breathing heavily as he glanced around.

"Nice job." The hedgehog saluted the fox with a nod.

"Thanks." Tails replied with a brief grin, before turning to Silver with the spark of an idea in his eyes. "I need your help with something."

Silver cocked his head. "What?"

"GUN's fighters are holding their own against the airships up there, but it won't be enough in the end unless we do something to help them." Tails began. "If we can get up to and inside of one of those airships, I'll bet I could hack into it's mainframe and give us control of it! I just need somebody to watch my back while I'm working on it."

"It's worth a shot." Silver judged quickly, levitating into the air. "Let's go!"

Arms raised defensively, the telekinetic hedgehog shot toward the chaotic battle overhead, with Tails following closely behind. All around them, GUN fighters dove and rolled to avoid the flak bursts that enemy airships were spitting out, while trying to find an opportunity to unleash their own arsenals.

"Stick close!" Warned Silver, swerving to avoid a flak burst. A GUN fighter exploded ahead of them, and the hedgehog acted quickly to shield them both as they flew through the debris, feeling the heat from the blast as they passed.

"We need to get to the bridge, on top!" Yelled Tails, pointing toward one of the larger ships in the vicinity.

Increasing his speed, Silver darted toward the ship in question, weaving his way through the tumult-filled skies with the young two-tail right on his heels. A moment later they were on top of the metal monstrosity, rushing toward the bridge. Strong winds gusted over the metal decking as the duo rushed forward, and alarms began to blare loudly as several armored eggpawn squads were released from slots in the ship's hull.

Silver turned his attention to the bots, pointing his companion onward. "I'll take care of them, you get to the bridge!"

"On it!" Cried the kit, rushing ahead.

Several eggpawns moved to chase the young fox, but were quickly stopped by a telekenetic shove, which knocked them clean off the ship.

 _You're not getting past me._

The other bots immediately fired their weapons at the hedgehog, and he jumped sharply to the side, sweeping an arm out in front of him and sending several more bots flying off the deck. Despite the already long battle, there was no shortage of energy now in Silver's movements as he fought on the deck of the airship, rolling beneath a laser blast and sending another enemy flying. The gusting high-altitude air filled him with a fresh vibrancy, giving new life to his limbs and new strength to his mind.

The last few bots were smashed against the deck, and a second later the white hedgehog was gone, his boots ringing harshly against the metal beneath them as he hurried toward the bridge. The door leading inside had been forced open already, and several bots lay in broken pieces on the floor. Tails was hunched over the main console, brow knit in concentration as his fingers danced with practiced rapidity over the airship's controls.

"I'm almost through the firewall." Announced the fox, not looking up from his work. "Just another minute, and we should be in."

Just then, the ship shuddered slightly, and Silver watched through the bridge viewports as a GUN fighter swooped low overhead.

"If this works, we should probably let them know we're on their side, so they stop _shooting_ at us."

"It _will_ work!" Tails replied with conviction. "Just one... more... second... and... Jackpot!"

The kit grinned triumphantly, turning to face Silver with a mischievous gleam in his eyes. "The Resistance has a battleship now."

Gloved fingers played over the control keys, and outside the bridge, the airship's main cannons turned in response. A moment later they opened fire with a brilliant flash, sending their payload streaking through the afternoon skies, and striking their target full-on. Silver couldn't restrain himself from grinning and pumping a fist in the air as he watched. The unsuspecting target, one of Eggman's smaller airships, erupted into flames and began to veer wildly, forcing nearby ships to break formation and perform evasive maneuvers. GUN fighters took immediate advantage of the enemy's disarray, flying close and unleashing their full fury.

"Yeah!" Cried the fox, watching the scene play out. "That'll teach them!"

"Brilliant work, Tails." Praised Silver, patting the fox approvingly on the shoulder before turning to focus once more on the battle outside.

"Now lets put this ship to some good use."

* * *

A powerful midair kick finished off the last couple robots in front of her, and Rouge landed gracefully in a crouch, glancing around in search of her next target. The communicator on her wrist beeped, and the voice of Tails greeted her when she activated it.

"Guess who just commandeered an airship?"

Rouge turned her gaze upward, watching in mild surprise as one of the Egg Fleet's battleships dropped out of formation, turning and firing its powerful cannons on the other ships of the fleet.

"Nice move, Foxboy. I'm impressed."

 _"I do my best."_ Replied the fox proudly, before continuing: _"It would be nice though, if you could maybe get GUN to stop shooting us? We're taking lots of friendly fire up here."_

"We wouldn't want that now, would we? I'll get them off your back, don't worry. In the meantime, keep up the good work. We're advancing down here, and if we keep it up we'll be able to run these bots out of town entirely."

"Thanks Rouge. We owe you one."

"Sure thing, kiddo." The bat replied with a grin, switching off the device and turning her focus back to the battle on the ground.

 _That kid definitely has his moments of brilliance._ She mused, tapping into her comm-link with GUN.

"Listen up boys! We've got a friendly in the skies now..."

* * *

Meanwhile, not far away at all, a gigantic metal body fell to the ground with a tremendous crash. What was formerly it's head was now nothing more than a mass of scorched wiring and bent metal, courtesy of the Ultimate Lifeform. Crouched atop his latest victim, Shadow's crimson gaze scanned the battlefield with a calm and deadly precision.

It still bothered him that Infinite was apparently not here, but at least for the moment it seemed that Eggman's army would be forced to fall back. GUN's timely arrival had contributed greatly to the struggle. He had caught short glimpses of Amy Rose and the Chaotix crew fighting, and the white hedgehog he had seen yesterday was doubtless nearby as well. But regardless, that group would never have been able to hold off Eggman's army without help. Even now, GUN tanks and mechs were advancing, and their enemies were beginning to give way.

 _Perhaps that is my cue to vanish. GUN probably wants me dead just as much as the Doctor does._

Another moment, and he would have vanished in a quick flash of chaos control. But something caught his eye at that moment, and he hesitated. Several hundred feet away, a white female bat cold be seen ripping her way through the remaining robots.

 _Rouge?_

A quick burst of power shot to his hover-skates, and he leapt through the air toward his teammate. Several well-placed chaos spears obliterated the robots near her, and the black hedgehog landed with a thud amid their remains. The bat had dropped into a defensive posture at his appearance, and her eyes widened as she recognized him. They both stood silent for a moment, staring at each other.

Finally, Shadow spoke.

"I thought you were dead."

The female held her defensive posture, and her eyes only hardened at his words. "You're back to finish the job, then? After what you did to me last time?"

His brow furrowed. "What?"

"I trusted you Shadow. And you know I don't trust easily." Her tone was rough, filled with hurt and betrayal.

"What are you talking about? I didn't..." He trailed off, feeling like a fool for not expecting or realizing it earlier.

 _Damn you, Infinite. Damn you._

"Rouge." He began, almost pleadingly. "I swear to you, I have never betrayed that trust."

Apparently, his words did not have their desired effect, as the bat's face contorted in anger. "The hell you haven't! I _still_ have the bruises you gave me in Westopolis!"

"Rouge, listen to me! That wasn't me, it was-"

"I _don't_ want to hear it!" She cried, trembling in anger. "How can you ever expect me to trust you again after the things you said to me?" Her eyes were shining with unshed tears now, and Shadow was at a loss for how to respond.

"I trusted you Shadow..." The female repeated brokenly. "I promised that I would be there for you no matter what. I would have been by your side until the end..." She stifled a sob. "I just didn't realize how little that promise meant to you."

The black hedgehog's fists clenched tightly as she spoke, with sorrow, confusion, and hurt warring in his heart. But overpowering it all, was a burning fierce anger. A pure, unadulterated rage, directed at the one who had taken his form and used it to destroy what good there was in his life.

 _I should have killed that Jackal when I had the chance._

He opened his mouth to speak, to say _something_ in his own defense, but as he stared at Rouge's hurt and angry expression, he just couldn't find the words. He dropped his eyes to the ground in defeat. Even if she was willing to listen, he had no proof to convince her. His most reliable ally had been turned against him.

 _I'm sorry Rouge... Sorry for everything I've put you through._

A long silence followed, broken only by the distant noise of the battle, which was now nearing its end. The sun was low in the sky now, and the robotic army was falling back under the pressure of GUN and the Resistance. Metropolis would stand free another day, but Shadow couldn't bring himself to care at this point. Unable to bear his former teammate's distrustful gaze any longer, the black hedgehog closed his eyes, mentally reaching for the familiar comfort of his chaos emerald's power. A moment later he vanished, leaving only a whisper in the wind behind him.

"Take care, Rouge."

* * *

Tear-stained eyes blinked as he disappeared, and the bat stared silently for a long moment at the place where he had stood, her sadness and confusion tainted by the sting of anger and hurt.

Eventually, her communicator sounded, and the voice of Silver informed her that Eggman's army was in retreat. But the bat hardly paid him any attention, her mind fully occupied with thoughts of Shadow's inexplicable behavior.

"We wouldn't have beaten them back without GUN's help." The white hedgehog was speaking. "So thank you, for showing up when you did."

The agent heaved a tired sigh, and turned her focus to the device on her wrist. "Don't mention it. That was the plan we discussed with Knuckles. I'm just keeping my word."

"Well, it seems to have been a pretty good plan, at the least." Replied Silver. "And speaking of Knuckles, we've updated him on everything, and he wants to talk with you."

Normally, the news of Knuckles wanting to _talk_ to her of all people would have brought a smirk to her face, or a teasing remark from her lips. Today however, after that battle and after the encounter with Shadow, she just didn't feel it. She felt drained, physically and emotionally. But unfortunately, there was still work to be done.

Glancing briefly over the wasted metal corpses around her, the bat unfurled her wings and began the flight up to Angel Island. Metropolis was spread out beneath her as she soared upward, and the agent paused a moment to survey it's condition in the fading light of the setting sun. The remains of Eggmans army had retreated to the west, and GUN had decided not to pursue them, working to secure and fortify the city instead. Several fires raged in the western edge of the massive urban sprawl, and the open land beyond was heavily battle-scarred and littered with metal corpses. But at least the city was still free, still standing. That alone made the day a victory.

Several more minutes of flight brought her to the edge of the floating island, where Knuckles stood waiting for her.

The guardian stared at her for a moment with crossed arms, taking in her dirty and worn appearance, and then he spoke solemnly: "I never thought I'd see the day where I welcome _you_ to my island."

The bat couldn't resist a slight smirk in response. "Its nice to see you too, Knucklehead."

The echidna grunted at the nickname, before speaking again. "I guess your plan to get GUN involved worked out pretty well."

She grinned. "Admitting _I_ had a good idea? Wow. How did those words taste coming out?"

"Like vinegar." Came the quick response. "Don't get used to it."

She managed a small laugh at the echidna's suffering, before sobering up again. "It did work though. The president himself has authorized full use of any and all necessary force against Eggman, and I've been assigned as the official liaison to your Resistance. Normally, GUN wouldn't be so keen on offering help to a group of mobian vigilantes, but this is an extreme situation, and I can be very... _persuasive_." She explained with a slight smirk. "Everybody recognizes the serious nature of this threat, now that Sonic is gone, and Shadow is... well..." She trailed off.

"A violent lunatic with amnesia again?" Supplied Knuckles.

"No!" The female replied without thinking. "Well, maybe... I- I don't know."

"What do you mean you don't know?" Retorted the echidna. "He's working for Eggman and he helped take out Sonic!"

"I just don't know!" She yelled back angrily, before shaking her head in frustration, and sitting down at the island's edge. "I saw him down there today, as the battle was waning. I know what he's done to everybody, and even to me, but... he was my friend, Knuckles. I _trusted_ him. Why is he doing all this?"

Knuckles sighed, before sitting down as well, his feet hanging over the cloudy abyss below. "I couldn't tell you Rouge. But, even if he was your friend before... he's obviously not very friendly right now. We can't afford to take any risks."

She looked down sadly. "I know that. But it still just doesn't make sense."

"There are a lot of things about all of this that don't make sense." Replied the guardian, staring out at the horizon's twilight glow. "So much has changed lately. What are we supposed to believe at this point?"

Rouge couldn't find the right words to answer, and a depressing silence reigned despite the recent victory, as they sat together under the darkening skies.

* * *

"He'll be back, you know."

Silver turned his gaze from the colorful twilight sky, giving Tails a confused look. "What?"

"Eggman, and his army." Replied the fox. "He never gives up."

The two were standing atop their newly commandeered battleship, which had survived the battle in fairly decent shape, thanks to Tails' expert piloting skills. They floated alone in the darkening skies, now that the Egg Fleet had retreated and the surviving GUN fighters had all landed.

"I'm sure you're right." Silver said at length, responding to the fox's assertion. "But at the very least, we've bought this city and it's people some time, and we've shown Eggman that we won't let him win without a fight. That counts for something, doesn't it?"

"It does, and I'm glad we won today." Tails began, idly twisting one of his namesakes as he continued on. "Its just that... I don't know. It doesn't _feel_ like we won a great victory, and I can't help but have a bad feeling about what's coming next. After all, we didn't even see Shadow, Chaos, or the masked guy here."

The hedgehog shook his head. "You do have a point. We managed to win today, but only because GUN showed up and took them by surprise. The next time, we won't have that advantage, and if a couple more powerful players arrive... well... there's only so much more we can handle."

"That's what I'm afraid of. Especially with Sonic gone." The fox confessed quietly. "Even though we won, I just have a bad feeling about all of this."

Silver remained quiet, but as he thought the matter over in his head, he couldn't help but feel the same sense of foreboding that had possessed Tails.

 _This war is just beginning -_ _what troubles does the future still hold in store for us?_

* * *

Far away from the drama surrounding Metropolis, at the end of a dim and forbidding hallway within a top-secret base, hoarse screams resounded from behind a tightly closed and locked door. Security cameras covered the hall and the door from every angle, and two highly specialized robots stood guarding the door, motionless and unresponsive to the cries of pain and terror issuing from within.

Eventually, the sounds quieted, and the door slammed open of its own accord. Pointed metal boots rang harshly against the steel floor, and a black gloved hand pointed to a shuddering and coughing blue hedgehog beyond the doorway. "Escort him back to his cell." Ordered a deep and distorted voice, from behind a pointed mask. The two robots immediately began their task, while the dark masked figure strode firmly down the hall.

"How did it go?" Questioned the one who had given him his power, and to whom he had sworn allegiance.

"His will is strong, but every being has their weakness. In time, I will break his spirt completely."

"Excellent." Declared the sinister voice of his master. "But you'll have to make time for that later. His _friends_ are putting up more of a fight than we expected. Get to Metropolis, and lead the next attack yourself. I want them _crushed!_ "

"With pleasure." The masked figure replied obediently, as the glowing ruby on his chest pulsed bright.

 _"All will yield to my power."_

* * *

 **Author's Note: S** **orry to all of you who wanted to see Shadow have an easier time... It ain't happening yet, that's for sure.**

 **I hope this chapter didn't seem too disjointed, there were a lot of characters and perspectives to fit in this short but important period of time. Rouge especially played a large role here, and her interaction with Shadow was the most intense portion for me to write, just because of how that affects the plot and characters going forward. And because I really want to explore the character's relationships in this story. Shadow and Rouge have always been a team, from the moment they were introduced, but now everything changes, and they have to deal with that in their own ways. It's going to be interesting later on.**

 **Anyway, all reviews, questions, and opinions are welcome as per usual. I'll have the next update out as soon as I can - the story only gets more intense from here on out, so get ready!**


	14. The Coming Storm

**AN - Ok ok, I know everybody feels sad for Shadow, but you'll have to wait a bit longer before finding out how he's doing. Sorry.**

 **Again, many thanks to my reviewers.**

 **Alexandria Prime \- Shadow always gets that sort of bad luck. But don't worry, he's tough enough to make it through. As for what he may or may not do in the future, I can't say. Far be it from me to spoil anything for you! **

**Infinite's Ruby \- Glad that scene got to you, I went through quite a few iterations of it before finally deciding I liked it. There's going to be a lot more diving into Rouge and Shadow later on in the story, and I wanted to get that interaction between them right.**

 **TheLastoftheRealOnes \- Yeah, you really won't see much of Sonic for a while, but just trust me when I say he's not having a lot of fun. :(**

 **Awdures \- Tails doesn't get enough love. And yeah, under normal circumstances, Rouge would be the first to doubt that Shadow had joined Eggman, But Infinite's trickery is nothing to sneeze at, and in the heat of battle, emotions can get in the way of thinking things through. But to say the least, Rouge and Shadow's relationship will be a very interesting part of the story in the future.**

 **endless-pastability \- "The calm before the storm" is a really good way of summing it up, actually. I'm glad you liked that chapter, and I hope this one is just as enjoyable for you!**

 **bajy , Extreme Light 9, & PetsnanaG \- Thanks for the reviews, and here's the next bit of story for you all!**

* * *

Chapter 13 - The Coming Storm

* * *

The morning after the battle dawned cool and clear, with a bracing wind sweeping over the hills from the north. The bright rays of the sun, firm and warm in all their early summer glory, beamed down on a sprawling city that against all odds, still stood tall and free. The Resistance (with GUN's timely assistance) had saved the city from Eggman's assault, but there was no time to rejoice. Neither was there time to dwell on the questions or forebodings of the evening before. The dawning of a new day brought important issues to light, and there was much work to be done.

Metropolis stood free, but victory had not come without cost. Several fires still raged in the western outskirts of the city, which had borne the brunt of the previous day's carnage. A few buildings had been completely demolished, several more were in precarious conditions, and countless others had at least minor damages. There were dozens of citizens with varying degrees of injuries, and many more whose homes or livelihoods had been ruined in the attack. To make matters worse, with the mayor and most of the city officials having fled before the attack, there was very little government left to maintain control or begin any sort of relief effort. GUN had stepped in to partially fill that void, if only to preserve some sort of law and order among the inhabitants, and to begin fortifying the city against future attacks.

The fact that the militaristic organization was even involved, let alone pledging to support a group of mobian vigilantes, spoke volumes as to the severity of the situation. GUN was a majority human organization, and seldom involved itself in dilemmas outside the borders of the United Federation, the government which funded and authorized it's operation. Their offer of help for the fledgling Resistance was... unusual, to say the least. This was an untested alliance, forged only by necessity in the face of a common enemy, and it would require compromise from both sides to work. To that effect, the commander of GUN would be landing in Metropolis at noon, to survey the situation and meet with the Resistance personally.

In the meantime, the Resistance was making preparations of its own. Silver, Amy, and Espio had joined in the effort to secure the city and provide aid to the wounded, while Tails, Vector, and Charmy made a return to the floating island, onboard the fox's recently captured airship. Unfortunately, they forgot to warn the island's rather paranoid guardian about their arrival, and Knuckles nearly suffered a heart-attack upon seeing the large red and yellow ship, emblazoned with enemy insignia, heading straight for his island. If it weren't for Tails quickly explaining the situation over the comm, the instinctive guardian probably would have jumped out and tried to punch the incoming vessel out of the sky.

* * *

"Next time you bring an enemy ship to my island, try letting me know you've captured it, _before you show up!_ " The echidna scowled into his communicator as the airship arrived at the edge of the floating landmass.

 _"Sorry!"_ Came the sheepish voice of the fox, as he maneuvered the vessel into a docking position.

"You'd better be..." Grumbled the guardian under his breath.

"My my, somebody sounds grumpy this morning." Teased the nearby Rouge, her confusion and worries about Shadow pushed aside in the light of a new day. "What's the matter, Knucklehead? Not a morning person?"

" _No_ , I'm just a little on edge because my island is still floating in the middle of a war zone!" The guardian responded in a huff, crossing his arms as he looked away from the bat. "And it doesn't help that Tails comes flying in unannounced on an giant enemy airship."

"Oh, relax a bit, Knuckie." Rouge smirked with a wave of her hand. "You have to admit, foxboy scored us a nice prize."

"Don't call me that." The echidna muttered, before glancing over the docked airship and admitting: "It's definitely something we can use." A moment later he added: "But he _still_ needs to call ahead next time."

Tails, Vector, and Charmy emerged from the ship a moment later, each of them dirty and bruised from yesterday's battle, but glad to be safely back on the floating island.

"It's good to see you're all in one piece." Knuckles remarked as he glanced them over. "Any signs of trouble down there today?"

"Nothing major." Reported Tails. "But Silver did spot what looked like a surveillance bot off to the north. If I know Eggman, he's definitely keeping an eye on us."

"Hmph. We can only hope he hasn't seen the island yet." The guardian muttered, glancing up at the clear sky above. "There's not enough cloud cover to keep us hidden well today. I don't want to stay here too long."

"Couldn't Eggman's sensors detect the island anyway? Clouds or no clouds?" Questioned Vector.

The echidna shook his head. "The Master Emerald's energy field keeps the island hidden from conventional sensors. If it didn't, everybody and their brother would be able to find us up here."

"We still can't be too careful." Warned Tails. "Eggman has found the island before, and he'll be able to find it again if he looks hard enough for it."

"Right." Agreed the guardian. "Like I said, I don't want to stay here for long."

"But we can't just leave the city alone!" Voiced Charmy. "What if Eggman attacks again?"

"That's not a matter of _if_ , it's a matter of _when_." Replied Tails. "He's nothing if not persistent."

"When and if Eggman attacks the city again," Rouge spoke, "GUN forces can be here to defend it and, if necessary, send out a distress signal."

"That will have to do." Affirmed Knuckles. "We just can't—"

He was cut off by the urgent beeping of his communicator, through which Espio announced:

 _"We've got incoming bots down here."_

* * *

The ninja's keen eyes scanned the northern horizon, staring closely at the incoming enemies.

 _"How bad is it?"_ Came the voice of Knuckles.

"It's not another army like yesterday." He reported coolly. "Several dozen eggpawns, perhaps a hundred at the most. Some buzz-bombers as well. Nothing we shouldn't be able to handle."

"If that's all, then let's head out and smash them now, before they reach the city." Silver spoke up from beside the chameleon.

"And if it's a ploy to get us to leave the city?" Espio questioned.

"GUN is still here, and we can make it back soon enough if there's a problem." The hedgehog replied.

 _"Go on then."_ Decided Knuckles. _"A few smashed bots now is less for us to deal with later. Let us know if you end up needing a hand."_

"Will do." Promised Silver, turning to Espio. The chameleon gave a nod, and the hedgehog lifted his hands, levitating them both down to the streets below, where Amy was busy helping to direct care for the wounded. A brief explanation later, and all three of them were racing out of the city toward the invaders.

"You two worry about the eggpawns." Directed Silver, his companions nodding their assent. "I'll take care of those buzz-bots."

Reaching their target, the three Resistance members prepared for the fight. Espio vanished entirely, and Amy summoned her hammer, as Silver's hands glowed bright and he took to the air. The robots turned to fire on their assailants, but they were a bit too late. Amy smashed her way through the Eggpawns in front of her, and Espio was a barely visible blur as the other pawns fell before his skillful and precise attacks. The buzz-bombers above them didn't fare any better, smashed to pieces by psychic energy or hurled against the ground with crushing force.

In a moment, it was over. The troop of robots lay in scattered pieces on the grassy turf, as the victorious trio poked through their remains.

"Why would Eggman send such a small force, when we beat off an entire army yesterday?" Wondered Amy.

Espio shook his head, unable to provide a reason, and Silver made no reply at all, rubbing his forehead as a mild headache manifested itself.

"Something doesn't feel right here..." He muttered after a moment, glancing over the ruined machines around him.

"What is it?" The pink hedgehog asked.

The white one shook his head. "I'm not sure. But I think we should get back to the city."

His companions nodded their agreement, and the trio headed back to Metropolis, unaware of the sinister eyes following their every movement.

* * *

The city was unchanged as they made their return, but Silver couldn't shake the unnatural and foreboding feeling that had settled within him. Something just felt _wrong_. Nevertheless, their task had been accomplished. The group of enemies had been demolished, and there was little time to dwell on vague feelings and impressions. The work to fortify and secure the city continued apace, and Rouge joined the trio already on the surface. Shortly thereafter, a squadron of armored helicopters was detected approaching the city from the east, signaling the arrival of GUN's commander.

The four mobians waited at the landing pad as the helicopter touched down, and the Commander stepped out. His look was exactly what you would expect from a man who had spent decades in the military. He bore himself with an air of unquestioned authority, and his steps were firm and measured. His short, greying hair blew wildly in the wind of the still-moving helicopter blades, and his eyes, one green and one brown, darted quickly over the mobians before him.

"Commander Tower." Rouge saluted as she stepped forward.

"Agent Rouge." He replied curtly, turning to face the others. "I assume you three are representatives of the Mobian Resistance."

"Representatives?" Silver repeated. _More like half of the the entire group._

"Indeed." Continued the Commander. "The negotiations must begin as soon as possible, we have much to discuss regarding this... joint effort."

"Negotiations?" Silver echoed again, confused. "Nobody told me we needed..."

"Of course!" Interrupted the pink hedgehog at his side, elbowing him in the ribs as she stepped forward confidently. "Amy Rose, official representative of the resistance, here under the authority of Knuckles the Echidna, at your service."

"Abraham Tower." The commander introduced himself with a firm nod. "Here on authority of the president of the United Federation himself. Is there a place we can discuss these matters?"

"Right this way." Amy replied diplomatically, quickly turning back to Silver and Espio. "You two." She directed authoritatively. "Keep things together out here while I'm busy." Then she lowered her voice, whispering: "And let Knuckles know he owes me for this." Then, straightening her back and turning around to face the commander again, she led him and Rouge into one of the nearby buildings.

Silver and Espio watched her go in silence.

"Huh." The white hedgehog finally managed. "I guess we'll let Knuckles know that he owes her one."

* * *

Leaving Amy and the Commander to their discussions, the duo returned to their work helping to fortify the city. Already, gun turrets had been mounted atop buildings, Beetle drones patrolled the outskirts, and several hundred mobians had been enlisted in the clean-up effort. The work would continue, but for now, the was peace in Metropolis.

That peace however, was only a fleeting illusion. Only a couple hours after the commander's arrival, GUN's robotic sentries detected an object headed straight for the city.

"We've got incoming from the north." A human voice announced to Silver and Espio through their comm units.

"What is it this time?" The white hedgehog asked.

"Were not sure." Reported the GUN agent. "But it's moving at supersonic speeds, and will reach the city within minutes."

Silver narrowed his eyes, and with a mental shove he shot into the air, heading off to the north. There, in the distance, a small figure was blazing over the terrain towards the city, leaving a long trail of dust in its wake.

Darting forward, the white hedgehog moved to intercept whatever it was. Even as he got closer however, all he could make out was a bluish streak moving almost faster than he could track. Flinging a hand forward, Silver raised a psychic barrier in the figures path, and prepared himself for a fight. The incoming blue streak veered aside at the last moment, avoiding the barrier, and curving around to strike the white hedgehog from the rear.

Silver shielded himself by pure instinct, turning around and finding himself face to face with a sleek blue robot. Another sudden headache beset him, as he took in the bot's appearance, and again he couldn't help but feel that something was just _wrong_ here.

The machine in front of him was built in the image of a hedgehog, but with some sort of jet turbine built into its chest. It's feet were red, formed like shoes, and it's hands terminated in sharply pointed fingers. It's joints were powerfully built, it's metal body gleamed brightly in the afternoon sunshine, and it's red irises glared sinisterly at him from within their black housing. It was plainly a more powerful and advanced mech than any he had fought before.

"What on earth are you?" The telekinetic hedgehog muttered to himself, as he glanced over the metallic figure. There was little time to wonder however, as not a moment later the robot zipped to the side and sent a metal fist toward his ribs. Silver launched himself backwards just in time to dodge, and the fight began.

The metal hedgehog moved _fast -_ faster than anything he had fought before - and it was all Silver could do to keep it at bay. Several times he tried to telekinetically grab the machine, but at such high speeds in such close combat, he couldn't manage a strong enough grip. A few bursts of energy forced it back slightly, but a second later it was on the attack again. A psychic push redirected a fist sent toward his gut, and another knocked aside a powerful kick. The bot charged at him, and Silver leapt into the air to dodge.

 _I won't be able to beat this thing in such close quarters._ He realized as the bot charged him again. _I need to fight it from a distance._ With a vivid cyan aura surrounding him, Silver clenched his fists and shot away from his assailant at high speed.

 _Let's see just how fast this thing is._

Twin sonic booms resounded over the landscape as Silver pushed himself faster, and the robotic hedgehog followed close at his heels. Faster, faster, he pushed himself, yet the untiring robot still followed doggedly behind him. He pushed himself even faster now, to the very limits of his speed, as the world moved around him in a blur. But even then, the indefatigable machine was faster, now just a few feet away from his heels.

 _One more trick..._

The white hedgehog braced himself, and reversed his mental push, stopping so quickly that he almost blacked out. The robot shot past him in an instant, curving around to charge at him again. But Silver was ready for it this time. His golden irises traced the bot's path, and with a sudden thrust of his palm, the metal hedgehog smashed violently into a telekinetic barrier. It spiraled out of control and landed hard on the ground, severely dented but astonishingly not destroyed.

"You are one tough robot." Silver muttered to himself as he raised a glowing fist, lifting his opponent in a tight psychic grip. "But why are you here alone? It's not..."

He trailed off then, as the pain in his head suddenly intensified. Until now it had been a mild ache. Now it was a full-on migraine. He shut his eyes against the pain, and when he reopened them, the robot was gone. His telekinetic grip held nothing but air.

"What...?" He gaped, staring at the empty space in front of him. "Where did it go? Why is my head-"

He cut himself off, as he heard footsteps behind him. He turned then, and came face to face with a sinister looking figure wearing a pointed mask, with an odd glowing ruby mounted in his chest.

 _That masked being Tails described..._ The white hedgehog realized, with no small amount of apprehension. _The one who defeated Sonic..._

His headache intensified again, as the dark figure stared at him in silence for a moment, arms crossed and head cocked to the side.

"Your mind is stronger than the rest." Came a deep and sinister voice from behind the mask.

Silver furrowed his brows at the unexpected pronouncement. "What?"

"Let's find out exactly _how_ strong it is..." The stranger continued, reaching out with a black gloved hand as the gem on his chest pulsed brightly.

Before he could protest, Silver was blinded by a flash of light, and forced to his knees by a now unbearable migraine. Scenes from his past, from the planet's ruined future, flashed like phantoms before his eyes, while the world twisted and spun beneath his feet. Closing his eyes against the images, Silver raised his hands to his temples, struggling to focus what energy he could through the pain. Finally, as his mind seemed ready to burst, the white hedgehog cried aloud: "Psychic Control!"

Mental energy lashed out in all directions, and the masked stranger growled in pain as Silver's headache vanished. Wasting no time, the white hedgehog turned and launched himself back towards Metropolis while his powerful enemy was distracted. He knew there was no way he could take on a being with such incredible and unknown power. Not alone, at any rate.

* * *

Espio and Amy were already waiting for him at the city's edge, as he arrived and gasped out the warning: "The masked one who defeated Sonic is here! Where are Rouge and Commander Tower?"

"The Commander just left, and Rouge is back on the Island." Amy explained. "But GUN is dug in, ready to fight no matter what. And if that masked creep is here, I'll make him pay for what he did to Sonic myself!"

Silver shook his head. "I admire your courage Amy, but that's suicide. Trust me, you're no match for him. Just maybe, if we all work together, we have a chance."

The pink hedgehog's eyes suddenly widened then, hammer materializing in her hands, and Espio's eyes narrowed as he glared at something behind Silver.

"Did you really think escape would be so easy?" Came the distorted and malignant voice of their enemy.

The white hedgehog took a deep breath, even as his adrenaline spiked. "I don't know what to expect." He answered as he turned around. "I just have to take what I'm given."

The masked one laughed then, a twisted and awful sound. "You have spirit! I will deeply enjoy seeing it crushed. Nothing can save you from what is coming."

Several GUN drones arrived then, homing in on the enemy and firing their lasers. But the dark figure batted them away like it was child's play, raising his hand as the drones were flung backwards.

"Everything you know is at an end." Declaimed the figure. "You cannot fight back, you cannot flee. Despair in that knowledge, before you perish!"

He raised a black gloved hand again, and the trio were sent flying backwards, deeper into the city. When they regained their bearings after impacting the street, the enemy was gone.

They stood in silence for a minute, catching their breath, when suddenly the ground began to vibrate beneath them. There was a sound from all around, a muffled rush like the crashing of waves on the shore.

"What now?!" Espio shouted.

The street below shook more violently, cracking in several places as geysers erupted from below, and citizens could be heard screaming in the distance. The rushing sound became a roar, as water erupted from storm drains and sewers. The formerly clear skies grew suddenly grey, as dark swirling clouds formed and coalesced into a stormy ceiling above the city, and rain began to fall.

"What in the name of Mobius is this?! Cried Silver, as his head began to throb again.

"No..." Breathed Amy, staring around with wide and panicked eyes, as a nightmare from the past was re-born before her eyes. The rain fell harder, as more geysers erupted from the streets around them, and the city began to flood. "It can't be!" She muttered. "The emeralds aren't... We took care of this... It's not..."

"Amy?" Silver questioned worriedly, as water rose quickly past their ankles. "What's going on?"

At that moment, the floodwaters swept inwards, toward the city center, and Silver quickly levitated his companions to higher ground atop one of the nearest buildings to avoid being carried away. As they landed, the white hedgehog could do nothing but gaze in awe-struck horror as a gigantic, writhing mass of water gathered in one of the flooded city plazas.

"No!" Amy cried out. "Not again!"

As they watched, that mass of water coalesced into a massive reptilian form, liquid water transforming into a sort of scaly skin around the behemoth, as it sprouted from the waves below and towered over the city. Huge liquid tentacles erupted from around the base of the strange creature, and heavy eyelids snapped open to reveal narrowed jade orbs. Twisting and writhing like a monstrous watery demon, the creature turned its gaze to the stormy sky above. Opening it's massive jaws, the beast let out a horrible, unearthly scream that shattered windows and struck terror into the hearts of humans and mobiles alike, across the entire flooded city.

* * *

 ** _Thunder, rain and lighting_**

 ** _Danger, water rising..._**

 **Author's Note: A whirlwind chapter, this one. A bit shorter than most so far, but with a lot of action, as well as introduction of a few plot elements that will be important later. I could have gotten this update out a bit faster probably, but Sonic Generations just got enhanced for Xbox one and, well... I've bit a tiny bit distracted.**

 **But anyway, Silver finally meets Infinite here, as well as having a short scrap with Metal Sonic. Those scenes were fun to write, especially from Silver's perspective, not really having met these characters before. So it will be interesting to build on that going forward.**

 **Another thing - Forces cheated us out of a Phantom Chaos boss fight, and we got giant Infinite snakes instead, for some reason. That looked cool and all, but come on. Not fair to tease Chaos like that and then never do anything with him. So here in this story, he's going to show up for more than 10 seconds, and actually be a serious threat.**

 **A couple quick trivia items, for those interested:**

 **"Abraham Tower" is the name given to the GUN commander in the comics, and in both the comics and the games, he has one green eye and one brown eye.**

 **Silver's move "Psychic Control" is from Sonic Rivals, where it is used to disorient opponents for a short time.**

* * *

 **As always, reviews, suggestions and opinions are welcome, and I will have the next chapter out as soon as I can. :)**


	15. Scream of the Storm

**Author's Note:**

 _116 reviews? I must say I never expected this story to be so popular. Thank you all so much for your support._

 _Ways \- Don't apologize, life gets in the way for all of us. I'm just glad you liked this fix enough to catch up with it again. :) / Chapter 10 pretty much sums up why Shadow is my favorite character to write. He just has such a depth of character and story to him, and he can walk the line between good and evil so finely. / As for the last chapter, I did think about including more of Amy and Abraham. I even had some stuff written out at one point. But it got to be too long and drawn out for what I wanted that chapter to be, so I ended up cutting it. But don't worry, you'll see a lot more of Amy going forward, she's actually a very important character in this story._

 _endless-pastability \- No, Metal Sonic can never win against walls. It is his curse. :P And yeah, Silver's interactions with Infinite are going to get pretty fun later._

 _Pocketmage \- I have seen the IDW series, and I love it. The characters are portrayed so well. I wont go into details, for fear of spoiling it to anybody who hasn't read it, but I did appreciate how they portrayed Amy in issue 2. Also, that same explanation for the wisps actually comes from Sonic Runners, but not many people really paid attention to that game. Fun fact. :P_

 _TheLastoftheRealOnes \- Silver's perspective to all this is unique, because it's new. I've actually enjoyed writing him more than I expected I would. And yeah, I like Forces as a game, but the whole Chaos thing was a bit of false advertising on SEGA's part. _

_ Alexandria Prime \- When will the gang will find out the truth? Stay tuned. ;) _

_Infinite's Ruby \- Well, if you like Silver, odds are you'll like this chapter too. Hope you enjoy!_

 _Thanks as well to: Extreme Light 9, bajy, PetsnanaG, Heroverse101, and Awdures. I'm glad you're enjoying the story!_

 _But now that all that is out of the way, here's what you've all been waiting for. (Sorry it took so long again!)_

* * *

 **Chapter 14 - Scream of the Storm**

* * *

Peals of thunder resounded over Metropolis, as lightning tore through the cloudy skies above, and cold rain fell in heavy torrents. The streets of the city were turned into veritable rivers, sweeping away anything or anyone unfortunate enough to be caught in their currents. GUN, for all it's vaunted military might, was powerless to struggle against this storm. Tanks, gun turrets, fortifications, foot soldiers - all was useless. The floods carried everything away with ease. Mobians and Humans alike desperately clambered atop anything sturdy enough to withstand the raging waters, even as the waves rose around them and the tall buildings wavered under the pressure of the tempest. Terror seized at their pounding hearts. What hope was there to fight against a storm of such supernatural strength? For there in front of them, at the center of this maelstrom, stood a towering mass of epic proportions and menacing shape. It was liquid, brought to life, and molded into an unmistakable form. It was the god of destruction itself.

* * *

"Perfect Chaos..." Amy breathed, staring in horror at the beast with her companions, from their perch atop a storm-battered high-rise. "No no no! How is this happening _again_?" She shook her head despairingly, her mind trying in vain to explain what her eyes were seeing. _Sonic fixed this! The emeralds aren't even here! What's going on?!_

"The questions will have to wait." Espio warned over the noise of the storm, not looking away from the terrible scene before them. "Regardless of how this is happening, it _is_ happening, and we can't just sit idly by."

"He's right." Silver agreed, suppressing a shudder as the rain soaked him through, and feeling that same mild headache again as he stared out at Perfect Chaos. "We have a job to do - defend this city and it's people as long as we can. You've faced this thing before, Amy?"

"Sonic did, but I was there."

"How did he defeat it?"

"He used the positive energies of all the chaos emeralds..."

Silver shook his head. "That's not an option for us now. Doesn't that thing have any weakness?"

"It has an organic brain!" Amy gasped as she remembered. "If we could get close enough to hit it, we might be able to do some damage at least!"

"Right there!" Espio yelled as the storm intensified, pointing toward the beast's massive head. Sure enough, there in a watery fin atop the creature's head was a small orange mass that almost appeared to glow in the darkness of the storm. "We need to strike right there!"

"Not we." Announced Silver as he stared at the target. "I can fly, I'm the only one with a good chance at getting close enough to hit it."

Turning to Amy and Espio, he directed them: "Let the others know what's going on. Knuckles probably shouldn't keep his island anywhwere near here. So let them know, and then do everything you can to evacuate this city. We have to save as many people as we can!"

"We can't let you fight that thing alone!" Protested Amy. "Sonic used all seven emeralds to beat it, and you don't even have one!"

"Unless you plan on swimming, you're not going to be much help!" Silver yelled back through the rain, shaking his head. "You can help me by evacuating the citizens. We're fighting to save people here. I'll do the fighting, you do the saving. Now go, I'll be fine!"

Amy opened her mouth to speak again, but Espio grabbed her wrist and led her down into the building below. "Call Knuckles now." The chameleon said firmly, as they disappeared inside.

Silver watched them go, then braced himself in determination, turning back to face his enemy as the rain poured down in sheets from above.

 _I'll be fine._ He told himself.

Then, as he watched a moment longer, one of the beast's massive tentacles slammed into a high-rise, impacting with terrible force and sending the building crashing down to the flooded streets below.

He shook his head, adding on to his last thought: _I hope._

* * *

Inside the recently hollowed out cavern on Angel Island (now the living quarters and storage area for the Resistance) Knuckles the Echidna stood gaping at the communicator on his wrist, mind struggling to catch up with what Amy had just told him.

"Say that again?"

 _"Perfect Chaos!"_ The normally cheerful hedgehog yelled through the static. _"Perfect Chaos is on a rampage through Metropolis right now! Silver is trying to keep it busy while we evacuate the city!"_

"How is that even-"

 _"I don't know!"_ Amy cut him off, her tone full of urgency and worry. _"I have just as many questions as you do, but they're going to have to wait! There are a lot of people in danger down here, and we need to get busy!"_

"Okay, okay!" The echidna responded with a shake of his head. "You guys do everything you can down there. I have to get the island out of danger, but I'm sending the others down to help you."

 _"Okay, just tell them to hurry!"_ The female urged, before adding quickly: _"I've got to go, we'll update you whenever we can."_

A burst of static ended the connection, and Knuckles groaned unhappily. _Chaos! How and why is Chaos here without me knowing about it?_ _Without a single hint from the Master Emerald_ _? From Tikal?_

His thoughts were interrupted as running footsteps sounded from the cavern entrance behind him.

"Something up, boss?" Charmy questioned, floating through the air beside Vector and Tails.

"You three need to get down to Metropolis." The echidna ordered without preamble. "Perfect Chaos is back, somehow, and we need to evacuate the city."

The trio stood and stared at him for a moment, in shock, before he snapped: "Nobody knows how or why, just get down there, now! Amy, Espio, and Silver need help, and I've got to get the island out of danger, so go!"

Shaking off their surprise, the group nodded quickly and set into action. They were out of the cave and dashing through the jungle in less than a moment, headed toward the island's edge.

Knuckles stood for a moment as he watched them go, feeling more concerned about this turn of events than he'd like to admit. But he couldn't stay idle for long. With Chaos near, Angel Island was in danger, and therefore the guardian had a job to do. Mouth set in a grim line, he ran off toward Hidden Palace.

* * *

Amy shivered as she and Espio stepped out of the building, and onto one of the many viaducts weaving their way through the city. The cold rain soaked them thoroughly, and the streets below them on ground level were transformed into raging rivers. Glancing up, the pink hedgehog caught a glimpse of Silver as he jumped from the building's roof, flying off in a cyan glow toward the monster at the center of this storm.

"Split up." Spoke Espio, drawing her attention back to their own mission. "We can reach more people faster that way."

She nodded in agreement. "Just be careful in this storm. We don't want to lose anybody today."

The chameleon smirked. "Same to you."

Then he was off, jumping from highway to highway above the floods below.

 _Alright Amy, there are people counting on you. No giving up until everybody is safe!_

Steeling herself, Amy ran off in the other direction, raising her hands to her mouth and calling out loud to any survivors. It didn't take long to find them. On top of cars stranded in flooded streets, or huddled on rooftops overlooking the scene, all over the city humans and mobians alike were clinging desperately to anything that could possibly withstand the waters. They all needed help, and Amy was determined to offer it.

To everybody within her reach, the pink hedgehog offered a helping hand away from the waves, and toward the hope of rescue.

"Get to higher ground, we're going to get you out of here!"

She held out the end of her hammer to mobians trapped in the currents, and helped carry children to the rooftops.

"Help is coming! Don't give up!"

But for every individual she pulled from the waters, it seemed like there were 10 more further ahead. In a city so massive and populous, how were they supposed to rescue everybody? She looked despairingly through the rain, as lighting flashed in the skies above, and thunder shook the ground. Shaking her head, she pressed on to the next survivor. It didn't matter how many there were, she would never stop trying to reach them all.

She was soaked through to the bone, but that didn't matter. Her limbs burned with exhaustion, but she refused to rest. People needed help, and it was her duty to give it. It was what her friends were doing. And it was what Sonic would have done. He would never give up, so neither could she.

* * *

Silver flew through the tempestuous skies, banking in a wide circle around his foe. Amy and Espio had told him to attack the brain, but they never mentioned exactly _how_ he was supposed to _reach_ the brain. Whenever he tried to swoop forward, Chaos always seemed to know exactly where he was, and would shoot bursts of energy in his direction to ward him off. Now, the beast's massive tentacles were making swipes at him whenever he ventured close, as if he was a fly to be shooed away.

 _This is definitely not how I expected this day to go._

He yelled in surprise as a watery appendage tore through the air in front of him, barely managing to dive down beneath it in time. Chaos roared, and another tentacle slammed down from above. Weaving aside, Silver turned away from the creature, putting some distance between them to give himself time to breathe. He was already tired, and the fight's constant strain on his power wasn't helping his constant headache.

The beast stared at him as he hovered there, one of its tentacles smashing into another building and sending it crashing to the ground, almost taunting Silver to make another move. Lighting split the skies around him, and the roar of the thunder was deafening. The cold rain poured down in sheets, soaking his fur and chilling him to the bones, but he ignored it. His mind was fully occupied with the massive enemy in front of him, and how he could possibly attack such a powerful foe.

 _If I could only get close enough._ He thought to himself. _But that thing always know where I am. There are too many tentacles for me to dodge them all..._

Suddenly, an idea presented itself, and Silver seized upon it. He cut off his power and began to fall toward the surface, lifting himself again at the last second to skim rapidly over the flooded streets, with glowing palms stretched out to his sides. In his wake, cars, destroyed robots, and pieces of collapsed buildings were all lifted from the waters and dragged along by his telekinetic power. Turning his face upward again, Silver and his newly gathered trail of debris shot high into the air toward Chaos. The beast opened its mouth, and bullets of pure energy shot toward the white hedgehog, only to be narrowly dodged.

 _My turn._

Swooping high, Silver spread his arms and gathered his arsenal.

"Take this!" He cried, flinging the rubble and debris at Chaos all at once, and from several different directions. The beast's tentacles tried in vain to bat away every incoming projectile, and Silver grinned.

 _Now!_

Launching himself through an opening in the monster's defenses, Silver darted forward while it was distracted. Raindrops suddenly felt like knives against his skin, as he pushed himself past the sound barrier and within range of the creature's vulnerable brain. He reached out with a glowing palm, and his psychic blast impacted it's target.

Chaos screamed then, twisting its body and knocking Silver aside. But the damage was done, and as Silver recovered himself, he watched the beast shake and writhe in pain. For a moment, the massive liquid body almost seemed on the verge of collapse, but the fight wasn't over yet. Chaos seemed to recollect itself, and issued another scream of pure rage as it's eyes locked on Silver.

The white hedgehog clenched his fists and readied himself, setting his face in a look of pure determination as he charged back into the fray.

"Come on, you monster!"

* * *

Amy glanced up to the stormy sky as she heard Chaos' scream of pain. _Whatever you're doing Silver, keep it up._

Turning her focus back to the the ground, the cold and tired hedgehog was about to head off in search of more survivors, when a familiar voice greeted her from behind.

"Need a hand, Pinky?"

Amy turned to Rouge as she descended through the rain. "I'd certainly appreciate it." She grinned through her exhaustion. "We need to get everybody out of the city. The Chaotix and I are getting survivors to the rooftops, and Tails is using the airship he captured to ferry them to safety."

"GUN has been working in the same way." Rouge revealed. "The hawk drones are pretty durable, even in this storm. We've fitted several with nets to lift survivors to the rooftops, where we have several helicopters working to fly them out of this mess."

"That's great news." Amy commented, relieved. "I was worried that we wouldn't be able to get everybody out in time."

"It looks like you've done enough." The bat encouraged. "We've swept for survivors through most of the city already, this is one of the last sectors we're searching." She paused for a moment, adding: "Whatever Silver is doing up there, it's been keeping Chaos distracted enough for us to finish the job down here."

Amy glanced upward again, shaking her head tiredly. "I still don't understand how or why Chaos is even here."

"Neither do I." Replied the agent. "But there's a lot of things I don't understand lately. For now, we should focus on getting the rest of the city evacuated."

Amy nodded. "Let's get going then."

* * *

Tails worked carefully from the bridge of his airship, maneuvering closely and precisely alongside the rooftop he was targeting, holding the ship steady as Vector and Charmy worked to bring the evacuees aboard. Straight out the window in front of him, the young fox could see the massive form of Perfect Chaos turning and twisting, its tentacles flailing wildly in an effort to swat down the tiny hovering figure that was Silver.

 _I really wish Sonic were here._ He thought worriedly. _Nothing about this makes sense._

"Everybody's on board!" Came a shout from Vector, startling him from his thoughts.

"Good!" He shouted back, fingers flying over the airship's control keys. "Heading to the next rooftop!"

Charmy buzzed through the door to the bridge a moment later, soaking wet from the storm outside. "The cargo bay is almost full, I don't think we'll be able to fit many more passengers."

"We shouldn't have to." Replied the fox, without looking up from the controls. "GUN helicopters are here now, helping with the rest. There shouldn't be many more people to evacuate."

Another moment of careful maneuvering, and the ship settled alongside the next rooftop.

"Go help Vector quickly." Directed Tails, with a gesture out the window at Perfect Chaos. "We're sitting a little too close for comfort."

The fox might have aimed his airship's cannons at the beast, but he remembered a time when Eggman had tried that same tactic, during the Perfect Chaos incident in Station Square. The Doctor's entire airship had been knocked out of the sky, with hardly an effort from the monster. So today, Tails had decided that it would be better to just not draw any attention to himself and his passengers.

"Everybody is on board." Vector announced a minute later, stepping onto the bridge with Charmy on his heels. "The cargo bay is packed, so I think we'd better drop off this load before going back to pick up any more."

"Almost everybody is evacuated." Tails informed the croc, maneuvering away from the rooftop. "GUN can handle the rest, but first we need to pick up Amy and Espio."

"I'll go get Espio!" Announced Charmy.

"And I can hold the ship in position up here while you bring back Amy." Vector suggested to Tails.

The fox hesitated for a moment. "You won't crash it, right?"

Vector feigned insult. "Crash? Me? You don't know who you're talking to, Tails. One time, I flew a-"

"Okay, okay." The kit relented, shaking his head. "I trust you. Just be careful."

A moment later, Tails jumped out from his vessel and into the storm, feeling the rain completely drench him within seconds. Charmy was right in front of him, heading off toward Espio, while Tails turned and tracked the beacon in Amy's communicator. Off in the distance to his right, Silver and Chaos were still locked in battle, and the fox couldn't help but feel a shiver down his spine as he heard the monster's scream.

* * *

Silver groaned frustratedly, swerving aside as a massive tentacle tried to end him. He had hit the brain several times now, but the creature still wasn't defeated. He was soaked through, freezing, and completely exhausted. And he still had the same infernal headache.

Another tentacle missed him by a few inches, and several energy blasts passed narrowly beneath him. "I've had enough of you!" He cried, flinging a powerful psychic burst at the next tentacle in his path. The white hedgehog flew straight through the watery appendage as it blew apart into mist, and was quickly regrown behind him.

At that moment, like the lighting that flashed around him, an idea sparked within Silver's mind.

 _Could it really be that simple?_

Dodging another tentacle, he turned his head to glance at the flooded and ruined cityscape around him.

 _It's worth a shot. This has gone on long enough._

Facing the monster again, Silver focused his power, shaking himself from the exhaustion that threatened to overtake him. The lines on his bracelets glowed bright, and he shot downward towards the confused mass of water that formed the creature's base. Slowing down just before impact, the white hedgehog took a deep breath, and plunged into the waves.

It was bitterly cold, and the waters churned so rapidly that Silver could hardly tell up from down. He stretched out his palms, forming a shield around himself to regain his bearings, then launched himself upwards inside the monster's body. There, just up ahead, was the brain. His lungs ached for air, but he pushed himself onward. It was nearly close enough to touch now.

Focusing all the extra power he could, Silver stretched out his hand. He held the floating brain in a powerful telekinetic grip, and _squeezed_ with everything he had.

Instantly, Chaos' massive jaws opened in a pained scream, and Silver shot out of the watery body, turning to watch in complete exhaustion as the monster writhed and twisted in pain. It's scream echoed over the entire city, and it's body spasmed. Finally, it's reptilian form disintigrated, and the liquid that had formed it collapsed into a massive tidal wave that spread out through the entire city.

* * *

Tails had just joined Amy and Rouge on the surface, when the last scream of the beast resounded throughout the city. Moments later, a tremendous rushing roar was heard, growing louder every second. The fox's eyes widened, and he grabbed Amy by the wrists, quickly lifting her into the air.

"Tidal wave!" He cried, rapidly climbing away from ground level. Rouge leapt after them, and seconds later a powerful wall of water roared underneath, sweeping away everything in it's path.

But just as quickly as it had come, it was gone, and all was quiet. Eerily quiet.

"The rain!" Amy suddenly shouted, breaking the silence. "It stopped!"

And indeed, the perpetual rainstorm had finally broken, and the late afternoon sun was just beginning to cast its golden rays through small holes in the dark clouds. The trio alighted on a nearby rooftop, quickly scanning the horizons. Perfect Chaos was gone. The storm had ended. The entire flooded city was as quiet as death.

A moment later, something ladded on the roof behind them with a thud.

"Silver!" Cried Tails and Amy in unison, turning and rushing toward the white hedgehog, who was laying on his back completely exhausted.

"Hey guys." He replied groggily and with closed eyes, only managing to raise his arm in greeting. "How was your day?"

"Not as hard as yours, I'm sure!" Tails admitted freely.

"Are you alright?" Worried Amy.

"I'm exhausted, I probably have a few cracked ribs, and I now hate water." Muttered the telekinetic hedgehog. "But on the bright side, I am alive, and it did stop raining."

A moment later he grinned, adding: "And my headache is gone."

His friends smiled, and Rouge crossed her arms with a smirk as she looked down at them. "I guess we shouldn't be underestimating you, Silver Boy. You just fought Perfect Chaos, without any emeralds, and survived."

The white hedgehog smiled wryly. "I wouldn't recommend it."

"But still." Commented Amy. "You beat it, we won!"

"I wouldn't go that far." Tails interrupted. "We beat Chaos, for now at least. But look at this city." He gestured to the flooded and storm battered ruins around them. "Metropolis is lost. There no way we can fix this right now. Not with Eggman still around."

"But we did save most of the city's population!" Amy pointed out. "And we're all still alive to fight another day."

"She's right." Silver lifted his head to speak. "We might have lost Metropolis, but we fought hard, and we can still win the war."

As he finished his sentence, the white hedgehog laid his head back with a groan, muttering: "Now just... 5 more minutes before we go, ok? I don't feel like moving..."

Tails grinned, lifting his communicator to call Vector. "Can you fly the ship over here without crashing it?"

* * *

Several miles outside the city, a dark masked figure stood with a communicator in his black gloved hand.

 _"He did_ what _?!"_ An angry voice issued from the device.

"He defeated the phantom Perfect Chaos. He is a far more serious threat than we anticipated. Almost as great a threat as Shadow."

 _"I give you virtually limitless power, yet you can't even beat a simple hedgehog!"_ The voice yelled. _"What good are you?!"_

"This power is _not_ limitless, Doctor, and you know it. It barely managed to maintain the Chaos phantom for as long as it did."

The voice from the communicator grunted. _"Who knows how long it will take to recharge after that. Still! The city is ours, right?"_

"It is."

 _"Then we can accelerate our plans."_ The voice cackled sinisterly. _"Soon enough, the ruby will be so powerful, that even you won't be able to mess things up! Now get busy!"_

The communicator switched off, and the masked figure clenched his fists. After a moment, he turned around to face the flooded city of Metropolis.

 _No._ He reflected, as he headed for the empty ruins.

 _Not Metropolis anymore._ He grinned beneath his mask.

 _Robotropolis._

* * *

 _Author's Note:_

 _Phew. This is probably one of the most action-packed chapters in the entire story. Hope you all liked it!_

 _A few notes though. For one thing, as I have said before, the phantom ruby is ridiculously powerful. Like, it's not even funny. Secondly, Sonic beat Chaos without going super in Sonic Generations, so that's why I don't see a problem with Silver doing the same thing here. And I am using Generations for most of the inspiration here, because even though the SA1 and Generations Chaos fights are similar, there are several differences, and SEGA has said that Generations is more of what they originally intended the Chaos fight to be, without being constrained by the Dreamcast technology of the time._

 _As per usual, and reviews, opinions, or suggestions are welcomed, and I'll be back with the next chapter soon! (Hopefully)_


	16. Questions

_Author's Note:_

 _Okay, next chapter is finally here. Big thanks to all those who reviewed, as always._

 _Guest \- Why wouldn't I? _

_SmashQueen \- Forces wasn't bad IMO, just mediocre. SEGA really wasted a whole lot of opportunity with it. I know they don't really have room in a game for a long and in-depth story, but they could have done so much better than they did. I feel like the last game where they actually took the story seriously was Sonic and the Black Knight, or Sonic Unleashed, and those are about 10 years old now. :/_

 _endless-pastability \- I knew somebody would enjoy that Silver callback. :) I think SEGA did try to give the Ruby a weakness, but the storytelling in the game was just so bad that it didn't explain anything well at all. So I'm endeavoring do better than them, and I'm glad it's coming off well so far._

 _ShadAmy1Fan \- First off, thanks for the big review. / When considering Sonic's torture, there are two options I see. 1 - Tying Sonic down and holding a chilidog just out of his reach. 2 - Use the Phantom Ruby, and really mess with him psychologically. SEGA, I'm guessing, just went with option 1. / As for Shadow, he has a lot to go through still and it won't be easy for him, but he's tough enough to take it. It will get better for him, eventually. / I love stories where Any has more to her character than "I love Sonic". Sure that's an important part of her character, but it has a whole lot more meaning when it's not the only thing she does. That's one reason I love her portrayal in the IDW comics so far. / I won't spoil anything regarding Tails, but just keep in mind, the main reason he was separate from the resistance in Forces is so he could have a side-quest with little Sonic. And since little Sonic isn't in my story, Tails role is going to be quite different than what it was in the game. / I agree, there are a lot of things the Archie cannon did better than the official cannon, and several little ideas in this story are inspired by that. / The way Sonic and the Resistance know nothing about Infinite and his power after 6 whole months is one of the more ridiculous parts of the game story, and that's something I'll be improving upon, as you'll see soon. / Lastly, I am doing well, and thanks for your concern. I'm not going to get frantic over anything, but I do want to speed up the pace of my updates whenever I can. I'm more impatient than anybody to get this story written, so I can move on to new ones, hahaha._

 _Pocketmage \- That is a big issue with the Ruby, and one I struggled with for a while myself. I eventually decided to go with the idea that it works in both ways, more or less. It can alter physical reality - to a degree, not the entire world at once - or it can take over a specific person's senses entirely to give them illusions or cause them harm. As the story goes on, I'll explain it all in more detail. Hopefully I do better with it than SEGA did, lol._

 _TyrantGold \- That's exactly my goal in writing this story. I'm glad I accomplished it with that chapter. Thanks for the review!_

 _TheLastoftheRealOnes \- Yeah, I definitely had to do something like that. Without some sort of limitation, the phantom ruby is virtually unbeatable. (Get it? _Virtually _? I'll just see myself out now.)_

 _Alexandria Prime \- I'm very glad you enjoyed it. In all fairness to the blue boy though, if Generations is cannon Sonic also defeated Perfect Chaos without any emeralds. Of course, Generations is a time mess, so maybe it never really happened. Or maybe nobody remembers it. Idk. I hate time travel, haha. _

_Anyway folks, here's the next chapter. A little shorter than most, but I think you'll enjoy it just as much._

* * *

 **Chapter 15 - Questions**

* * *

Golden eyes opened drowsily, and Silver groaned as sleep left him, feeling all the bruises and exhaustion of the previous day catching up with him.

"How are you feeling?" A voice asked from nearby.

The white hedgehog turned his head at the sound, taking stock of his surroundings. He was back on Angel Island, resting on a bedroll on the floor of the Resistance cavern. His few wounds from the battle were cleaned, and there was a bandage wrapped around his injured ribs. Amy and the Chaotix were also stretched out on their own bedrolls nearby, still asleep in the dim early morning light that reflected through the cavern's entrance. Tails alone was awake, sitting atop his own bedroll and silently tinkering with a communicator.

"I'm... just tired and sore, I guess." Muttered Silver, finally answering the question. "How long have I been out?"

"Only since last night." Replied the fox, not looking up from his work. "You dozed off on the airship during the trip back here. Vector brought you inside and Amy helped take care of your injuries. She was exhausted too, though." He paused. "We all were by the end of it yesterday."

Silver grunted as he sat up. "Where's the island heading now?"

"Back out west, over the ocean again." Informed Tails. "Knuckles didn't want to stay above land any longer than necessary."

"And from there?"

"Who knows." The fox shook his head. "I think Knuckles plans on staying out here for a while. We could all use some time to rest and recover."

"I won't argue with that." Muttered the hedgehog. "But we can't stay idle for long. Especially with Eggman controlling Metropolis now. Every second we waste, he has time to get stronger."

"But is there really anything we can do at this point?" Questioned Tails, finally looking up from his tinkering. "Sure, you beat Chaos, but we lost Metropolis. We lost Westopolis. We lost Sonic..."

"There's _always_ something we can do Tails." He reassured the fox. "Don't give up hope now."

"It's just hard." The kit muttered. "How much more are we going to lose in this war? How many friends will I lose like I lost Sonic?"

Silver shook his head. "It doesn't matter what we might lose in this war, Tails. Because if we don't fight it, if we lose this war itself, we lose _everything._ Believe me, I know."

The fox sighed in resignation. "I know that too. It's just so hard to see the hope in all of this. And it's hard being without Sonic. He would never give up hope."

"We'll find him Tails." Promised the hedgehog. "If he's still out there, somehow we _will_ save him."

"He _is_ still out there." Came another voice from nearby. Amy was awake now, sitting on her bedroll and rubbing her tired eyes.

"I know he's alive." She repeated confidently, as she shook her drowsiness off. "We just have to find him."

"How can you be so sure?" Tails questioned.

"I just am." The pink one replied, as if that explained everything. Walking over to join them, she continued: "I don't know where he is, or what might be happening to him, but I _know_ he's alive."

Tails just shook his head at the girl's illogical response. "Either way." He remarked. "There's nothing we can do at the moment. We have no leads on what might have happened to him after I... after that day in Westopolis."

"We don't even know what's been happening right in front of us." Silver pointed out. "I fought Perfect Chaos yesterday, something you were all convinced had been taken care of years ago. How did that happen?"

"Without the emeralds being seen, no less." Added Tails.

"And that masked creature." Continued the white hedgehog. "The one you said was there when Sonic was defeated, he was there yesterday as well."

The fox's eyes widened. "You saw him?"

Silver nodded. "His power is something incredible... like nothing I've ever encountered before." He explained. "I don't even know what it really is, but I know I barely escaped my first encounter with him."

"I saw him knock those GUN drones away without even touching them!" Amy spoke up.

"How did he do that, I wonder?" Murmured Silver. "Where did he get such power?"

"For that matter, what kind of a being is he?" Tails questioned as well. "And why side with Eggman?"

"And what brought Chaos into all of this?" Added Amy.

A long silence was the only answer to their questions, and the trio shook their heads despairingly.

Silver let out a long sigh. "Too many questions, and too few answers."

* * *

Meanwhile, elsewhere on the island, those same questions were also plaguing Knuckles. But unlike Silver, Amy, and Tails, the guardian actually had an idea for finding a few of their answers. He had left the cavern early that morning, and was currently winding his way through the jungle toward the empty emerald shrine, and it's secret passage down to hidden palace. The air was cool and calm as he trod firmly onwards, and his unique senses were precisely attuned to the ancient environment around him. As he approached the shrine, he let out a long and exasperated sigh, sensing a familiar presence already there.

"What are you doing on my shrine?" He called out wearily, as he stepped into the clearing.

"I just thought I'd keep an eye on it for you, Knucklehead." Answered Rouge, as she glided down from above. "But where did the emerald go?"

"Wouldn't you like to know." The guardian muttered as he tapped his foot impatiently. "It's safe, that's all you need to know."

"Awww, Knuckie." The bat brought a hand to her heart, feigning hurt. "Don't you trust me yet?"

"No."

"You're no fun."

The guardian shook his head. "I've got things to do, Rouge. Things you can't be around to watch. Go bother somebody else."

"Things to do?" Echoed the bat, not moving from her position. "Well now you've got me intrigued."

"I'm not kidding Rouge. Go away."

"You're only making it more tempting to follow you."

"Leave. Now."

"You can't make me."

He raised his fists, angered. "Wanna bet?"

Rouge shook her head. "Are we really gonna do this again? You'll fight me, we'll both end up bruised, and nothing will change."

The guardian frowned.

"I'm a spy, Knuckles." She continued with a wry grin. "You know you're not going to stop me from following you."

"You _are_ a spy." The echidna replied, crossing his arms. "You're also a thief. And that's exactly why I don't want you following me."

"Look, Knucklehead." The bat said firmly. "If we're going to work together in this war, you're going to have to trust me a little. I worked hard, dragging GUN in to help you in Metropolis. If I hadn't come, where would your little resistance be now?"

Knuckles frowned deeper.

"I promise, I'm not going to steal the emerald, not at a time like this." Vowed Rouge. "Even if I did, where would I take it? I'm not stupid enough to risk the emerald falling into Eggman's hands, so as long as he's a threat, I _won't_ be." She held out a gloved hand in an offer of truce. "Deal?"

Knuckles eyed her warily, hesitating.

"Come on," she almost begged. "don't you think I've earned just a little bit of satisfaction for my curiosity?"

Groaning aloud, the echidna grasped her offered hand. "Fine. But you stay where I can see you, and you do exactly as I say. No buts."

"Whatever you say." The bat replied with a grin.

The guardian just shook his head. _I am so going to regret this._

* * *

As Knuckles pushed past her with a frown, Rouge couldn't help but feel an amused satisfaction rising within her. She hadn't expected the stubborn guardian to give in so easily. She had of course meant it, when she said she wouldn't try to steal the emerald at a time like this. But the wily batgirl hadn't made any promises not to steal it after Eggman was defeated.

 _If Eggman is ever defeated._ The pessimistic side of her personality warned.

She shook her head as she turned to follow Knuckles. Thoughts like that were useless to her. There wasn't time for her to dwell on the negative. Right now, it was time to see just what kind of secrets the Knucklehead was trying to keep from the world.

The echidna shot a warning glare at her as he opened a hidden door in the side of the emerald shrine, not-so-subtly letting her know he would be keeping a watchful eye on her. She responded only with a smirk, following behind him as he walked through the doorway and began traversing a long dark staircase down into the bowels of the island. The door swung shut behind them, and the sunlight from the surface world was shut out, but the ensuing darkness was not complete. Glowing crystals were embedded within the stone walls on either side of the stairway, casting a dim glow throughout the passageway. The pair's steady footsteps were the only sounds to be heard, and they continued downward in terse silence.

"Where are we going?" Rouge asked aloud, after several long minutes.

"Hidden Palace." Knuckles answered quietly, without turning his head. "It's where I'm keeping the emerald right now, as I'm sure you've guessed already."

The staircase ended suddenly, opening into a wide and finely decorated room. It's walls were covered in polished stones of green, purple, and blue, and the same luminous stones were embedded within them in marvelous patterns. Crystalline formations hung delicately from the ceiling, spiraling in ornate patterns down the walls. But apart from the splendor of it's decor, the room was barren. There was no furniture to speak of, no other passage into the room aside from the stairway they had just traversed. It seemed to be a dead end.

Rouge glanced at the guardian with a raised eyebrow, but he simply ignored her. Walking to one side of the room, he closed his eyes and ran a gloved hand gently over the ancient walls. His palm brushed against a hidden trigger, and a portion of the floor slid open near the staircase. Turning around with a solemn expression, Knuckles gestured for her to follow him as he slid down through the new passageway.

A moment later, Rouge was through the passage as well, staring in wonder at the magnificent scene around her. The room she had just left was nothing compared to this. She and Knuckles were standing in a massive cavern, the limits of which Rouge couldn't discern. Precisely sculpted columns supported towering ancient structures, covered with smooth, ornate stones and decorated with large jewels. The glow of the luminous crystals reflected off every polished surface, shimmering and reflecting, filling the cavern with a soft and beautiful light. Murals and writings covered the walls, depicting scenes of crisis and triumph, or of destruction and woe. They were all relics of a civilization almost completely lost to history, a civilization whose only living member was standing there next to her, with crossed arms and solemn expression.

"What is this place?" She murmured in awe.

"The Hidden Palace." Knuckles spoke, glancing over the silent splendor of the cavern. "It was built not long after Chaos was first enraged by my clan, thousands of years ago"

He walked slowly through the cavern, with Rouge close behind him, as he continued speaking: "After that incident, Chaos was sealed within the Master Emerald, and this island was ripped from the ground below. Afterward, the few surviving echidnas took it upon themselves to guard the emerald, to prevent such a catastrophe from ever happening again. They sculpted and expanded this cavern, creating the ultimate hiding place and shrine for the emerald."

He stopped for a moment, staring up at a large mural on the wall next to him.

Rouge glanced up at the mural as well, her brows furrowing as she examined it closer. There on the wall, a suspiciously familiar figure was depicted as reaching for the Master Emerald. Facing off against it was a smaller figure, spiky and blue, and enveloped in a golden aura.

"Is that...?" She breathed out in disbelief.

"Sonic and Eggman." Confirmed Knuckles, deep in reflection.

It had been so long since the events of the mural had played themselves out in real life, and he had grown so much since then, Looking back, he felt ashamed that he hadn't seen through the Doctor's lies sooner.

* * *

 _He was breathing heavily, and his body ached as he stared angrily at the blue hedgehog in front of him. His foe was grinning, wagging a finger. "You're pretty slow in the head, if you think I'm the bad guy here."_

 _He growled, and charged at the hedgehog again. A moment later a spiky blue ball slammed into his side, knocking him to the ground in a heap. The hedgehog stood there again, with that stupid grin still on his face._

 _"You're stubborn, I'll give you that."_

 _Suddenly, a loud crash interrupted the combatants. The energy field of the emerald changed dramatically, and Knuckles felt the whole island begin to fall. With wide eyes and a terrible pit welling in his stomach, he pushed past the bewildered hedgehog and toward the emerald altar._

 _There was Robotnik in his machine, ripping the Master Emerald from its rightful place. How? Why? What was the doctor doing?_

 _"Robotnik! Put that down! What are you doing?"_

 _He leapt for the emerald, trying to pry it from the machine's iron grip. A moment later fire raced like lighting through every nerve of his body, and he fell to the ground, his body wracked with painful spasms._

 _He woke a moment later, to see the hedgehog kneeling next to him with concern in his eyes._

 _"You okay?" He asked simply. As if the past was forgotten already. As if he had already forgiven Knuckles for relentlessly trying to kill him. Just who was this hedgehog?_

 _It didn't matter. Only one thing did._

 _"The Master Emerald..." He muttered, shaking his head and getting up on unsteady feet._

 _"We'll get it back for ya!" The hedgehog announced confidently, jerking his thumb toward himself and the young two-tailed fox behind him. "Robuttnik can't stop us!"_

 _He spared a moment to glance searchingly at the two strangers. Could he trust them? His spasming and exhausted body reminded him that he didn't really have a choice. Summoning what strength he could, he led the way toward the teleporter, gesturing for them to follow._

* * *

"Knuckles!"

The echidna shook his head from the memories, glancing over to Rouge. "What?"

"You completely zoned out, Knucklehead."

He glanced back at the mural for a moment.

"Just... memories. That's all."

The bat eyed him suspiciously. "I'm not the first one to visit here, am I?" She asked knowingly.

The guardian shook his head. "Sonic and Tails found their way in here, through the lava tubes. I was in the middle of fighting Sonic when Eggman took the emerald. That's the first time I realized he tricked me."

Rouge sighed. "You had a mural here foretelling the whole thing, and you _still_ trusted Eggman?"

Knuckles crossed his arms defensively. "It was my first ever interaction with another living being, and I've learned from it." He turned his back to her and continued walking. "We're not here for a tour. Come on."

Rounding a corner, the duo came face to face with the shrine itself. There on a wide open platform stood 8 large and ornate pedestals. Seven of them held giant dark stones shaped like emeralds, and they were arranged in a circle around the middle pedestal. That one was larger than all the rest, and upon it rested the Master Emerald itself. It's powerful light shone throughout the cavern, shimmering and pulsing in a way that seemed almost alive.

As they approached the Master Emerald, Rouge's hand lifted of its own accord, reaching out carefully towards the magnificent gem. Knuckles slapped it aside at the last moment, shaking his head. "Go sit over there and be quiet." He ordered, pointing to one of the giant stone emeralds.

Rouge shot him a sullen glare as she remembered her side of the deal, before reluctantly obeying. "What are these things?" She wondered aloud, as she jumped atop one of the stony forms.

"They're just rocks." Replied the guardian exasperatedly, not gazing away from his emerald. "You can steal as many of them as you want."

Rouge stuck her tongue out at the guardian's back, crossing her arms. Knuckles wasn't even paying attention to her, shifting to sit down cross-legged in front of the emerald, resting his hands on his knees and closing his eyes in meditation.

Silence reigned for a long moment in the vast cavern, until Rouge spoke and shattered it.

"What are you doing, exactly?"

Knuckles sighed, not opening his eyes. "You might find out, if you could stay quiet."

The bat rolled her eyes, complying.

Another long silence passed, and Rouge began tapping her foot.

"Quiet." The echidna commanded.

The bat opened her mouth to protest, but she had scarcely gotten a word out when Knuckles turned around angrily. "I swear, Rouge. You wanted to come down here. If you don't shut up right _now_ , I'm going to drag you back to the surface, rip out your wings, and then kick you off the island. Got it?"

"A little harsh, don't you think?"

Knuckles glared at her, and she wisely stopped talking.

The guardian breathed out deeply, resuming his meditation and sinking deep into thought and memory.

He focused his mind, diving deep into his connection with the emerald. The world around him fell away, and he felt the energy of the gem weaving and twisting throughout the entire island. Eyes closed tightly, gloved hands resting on the surface of the large gem, he silently willed the emerald to grant his request.

 _I need guidance._

 _Help me, Master Emerald._

 _Chaos has returned._

 _I need to talk to her._

For a few long moments, nothing happened. Then without warning, the emerald flashed brightly, illuminating the entire cavern. Brilliant tendrils of energy swirled within its crystalline structure, coalescing into a peach-colored orb of light, rising up from within the gemstone. The orb hovered there for a moment, just above the glowing rock. Then, in a flash of light, it vanished. In it's place atop the emerald stood a beautiful young echidna girl, dressed in ancient tribal fashion, and wearing a golden band on her forehead.

Her deep blue eyes gazed down at Knuckles, gentle and full of kindness. Clasping her hands together, as a smile broke out on her face, she spoke softly:

"Hello, Guardian."

* * *

 ** _Author's Note:_**

 _I couldn't very well leave her out of this, could I? Not when Chaos is supposedly involved._

 _Anyway, I hope you all enjoyed this chapter. It was a lot of fun to write, and there are a bunch of little nods to S3 &K in there. _

_It's been a while since a chapter focused mainly on Knuckles. I know a lot of people treat Knuckles as stupid or just unintelligent, but I don't like to see him that way. He used to be pretty gullible, but only because he was so inexperienced in dealing with others. I treat him as if he's grown over the years, and learned from those mistakes. And as I tried to show here, those mistakes are important events, important lessons in his life. They're events that he don't want to forget or repeat._ _And Rouge... Well, Rouge is Rouge. You never know what she really wants until she gets it._

 _Also, sorry to disappoint all of you who are waiting for another chapter about Shadow. You'll see more of him soon, but his story is a bit separate from that of the Resistance, and I don't want to break the flow of this narrative by skipping over to him too quickly. He'll be back soon enough though, don't worry._

 _As always, reviews, suggestions, and opinions are welcome, and I'll be back with the next chapter soon!_


	17. Wisdom of the Past

_**I'm back!**_

 _Sorry this update is so late, life got pretty crazy there for a bit, and I wasn't able to give this the focus I wanted to. But here it is, better late than never!_

 _Thanks again to all my reviewers, your support means a lot._

 _SmashQueen \- Infinite could create a lot of the things you've mentioned, and without spoiling anything, I will say that this story will have him create more than just the 4 replicas he did in Forces. I do think there's a limit to how far he could go creating duplicates and still be believed. If he went around with a Sonic clone that acted like a jerk, or something like that, people would catch on to it pretty quick. I'll go into this in more detail later on, but it's only the Shadow clone that Infinite really cares about, because it's Shadow who he really hates the most. Anyways, thanks for all the grammar tips, they're quite useful since I don't have a beta reader or anything for this story. I'm glad you're enjoying the story, and I hope you stick around till the end of it. (Because it WILL get finished, eventually.) :)_

 _Awdures \- Glad you enjoyed it. Hidden Palace doesn't get enough love, and neither does Knuckles character. He's grown a lot since he first met Sonic, and I love to go back and reflect on that, and how it affects his choices now. _

_endless-pastability \- Very happy you liked it. And don't worry, there's going to be a lot more Rouge-Knux interactions in this story, they're a lot of fun to write. :) Anyway, thanks for the constructive criticism, I'm glad to know about that so I can improve on it._

 _Mitha Sentro \- You're right, it is Sonic 3 (& Knuckles). And there's no mistake, Tikal and Rouge are in this chapter, continuing off from right where the last one left off._

 _MobiusHero \- The most impatient one here is me, lol. I want to get these chapters coming out faster, but at the same time I get busy, and also I don't want to rush because I want to keep it as high quality as I can. So, thanks for being patient. _

_ShadAmy1Fan \- I think I mentioned Classic not being here in a note after the prologue chapter or something, I probably could have advertised that a little better, lol. I'm glad you're enjoying the story, and yes, you'll see more glimpses of Sonic and what he's going through. I'm not going to detail the torture so far as to make this fic M-rated, but it won't be glossed over like it was in the game, no way. It will be interesting for me to be writing that later on, because going through something like that adds a new level of depth to a character, a level we haven't really seen from Sonic before. Shadow has that depth, and that's why he's one of my favorite characters as well. Anyway, I am doing well and I thank you for asking. Hopefully this chapter is worth the wait for you!_

 _Thanks also to Alexandria Prime, bajy, & Infinite's Ruby \- I'm glad you're enjoying the story and I hope this chapter is just as exciting for you!_

 _Without further ado, here is the next chapter for you all. This one gets pretty deep._

* * *

 **Chapter 16 - Wisdom of the Past**

* * *

Knuckles glanced upward as the brilliant light above the Master Emerald gradually faded, leaving only the shimmering form of a familiar echidna girl.

"Hello, Guardian," she greeted respectfully, with her hands clasped at her waist and a soft smile on her face.

"Tikal..." He breathed out in awe, silently thanking the emerald for allowing him to speak with her. "It's good to see you again."

"The pleasure is mine," replied the girl, levitating gently down from above the emerald.

Rouge hopped down from her perch atop the stone emerald an instant later, her teal eyes shifting back and forth between the two echidnas as she sauntered over to them. "Mind introducing me to your friend, Knuckles?" She asked, glancing at the guardian with a raised eyebrow. "I know there's an interesting story here. It's not everyday the Master Emerald spits out an echidna girl."

Said echidna girl cocked her head to the side as she stared at the unfamiliar figure, eyes glancing over her in curiosity. Knuckles just shook his head. "Rouge, this is Tikal. The one who first sealed Chaos inside the emerald all those years ago, and helped us defeat it when it attacked Station Square. Tikal, this is Rouge. She's really just here to bug me."

Ignoring the indignant protest from Rouge, Knuckles turned his full attention to the ancient echidna girl in front of him. "I'm afraid I've got some bad news."

"I suspected as much," Tikal sighed, before continuing wryly: "Otherwise you would not have asked to speak with me."

"Well... I..." he began, but she cut him off with a gentle hand on his shoulder and a reassuring smile.

"Tell me, what troubles you Knuckles?"

"Chaos," he answered bluntly, and Tikal's eyes widened in surprise. "Chaos is back, and we don't know how or why. I figured that maybe you could shed some light on how this happened."

The girl's brow furrowed. "What do you mean, Chaos is back?"

"I mean, Chaos is on the loose again, working for Eggman again, and destroying cities again." He shook his head in frustration. "And as if that wasn't hard enough to explain on it's own, it achieved its perfect form yesterday - _without this_!" He produced the blue Chaos Emerald from within his spines, holding it out for Tikal to see as he searched her face for some sort of explanation.

"Wait a minute, how long have you had _that_?" Interrupted Rouge, eyes drawn like magnets to the glowing gemstone.

"I've had it since before this whole mess even started." The guardian answered exasperatedly. "And no, you can't have it."

"I wasn't even going to ask for it!" She protested angrily. "I'm just wondering why you never told anybody that you had it."

"Because it's safest if it stays with _me_." He asserted firmly, shifting his attention back to Tikal, who had been completely silent since his words about Chaos. Her face showed visible confusion, brow furrowed and mouth set in a frown as she stared at Master Emerald, deep in thought.

"Tikal?"

She was silent for a moment, before turning her gaze back to him and shaking her head.

"Knuckles..." She began slowly, "Chaos is _still_ in the Emerald."

There was a long silence.

"What...?"

Tikal turned toward the glowing emerald again, placing her hand on it's smooth surface. "If he had left, and joined Eggman for some reason, I would know about it." Light flashed from the gem beneath her hand, and a moment later Chaos itself was standing there, in it's basic form. Knuckles and Rouge both instinctively took a step back, raising their fists, but Tikal waved away their concern. "He hasn't gone anywhere, Knuckles. He hasn't joined Eggman, hasn't destroyed anything."

Slowly lowering his fists, the guardian warily approached the watery creature. Chaos watched him closely, but remained motionless atop the emerald.

"Then how do you explain what happened yesterday?" He asked in confused frustration. "How do you explain what we saw, and the damage it caused?"

"Whatever that was, it wasn't the real Chaos."

"Wasn't the real..." murmered Rouge, eyes wide.

"How could it not be real?" Knuckles shook his head in disbelief, glancing from Tikal to the water god atop the emerald and then back again. "If it wasn't real, then what _was_ it? Another Chaos? A creation of Eggman's?"

"It's possible." Rouge spoke up after a moment. "Gerald Robotnik created artificial chaos robots half a century ago, what if Eggman simply created something beyond that?"

"A creation as powerful as Perfect Chaos?" Knuckles wondered. "How could he power something like that, when we know he doesn't have all seven emeralds?"

"I don't know," conceded the bat, "but if it's true that the Perfect Chaos we fought yesterday _wasn't_ the real Chaos..." Her gaze shifted to the silent watery creature atop the emerald. "If Eggman is capable of creating something like that, we could be in a whole lot of trouble."

A long silence followed, broken only by Knuckles heaving a long sigh. "Why couldn't there just be a simple answer?" He muttered.

The communicator on Rouge's wrist beeped suddenly, shaking them all from their troubled thoughts. "Its GUN." The bat reported after a quick glance downward. "I should take this."

"You know the way back to the surface, right?" At her nod of affirmation, he continued: "Go. I'll catch up with you, and we can discuss this news with the others later." As she turned to leave, he issued one last warning: "No touching anything on your way back! If I find out you've taken _anything_ from these ruins..."

"You'll rip out my wings, and throw me off the island. I know." The bat answered with a smurk. "Don't you trust me, Knuckie?"

The guardian groaned at the nickname. "Just go already."

Rouge grinned, winking flirtatiously at him as she sauntered off.

"Rip out her wings?" Tikal questioned as she watched the bat leave. "Who is she, exactly?"

"She's a spy and a thief," the guardian grumbled, crossing his arms.

"Aaaaand?" Tikal pressed, sensing more to the story.

"And, she's a friend." He admitted grudgingly. "She's been helping us fight against Eggman."

The echidna girl nodded, deep in thought. "You trust her enough to know the location of the emerald?"

"I trust that she won't risk stealing it at a time like this." He spoke carefully. "Not when it could fall into Eggman's hands, not with the world at stake like it is."

"And the world _is_ at stake?" Questioned the girl. "As guardian of the emerald, I hope you have not joined this conflict lightly."

"I joined _because_ of the emerald." Knuckled defended. "A white hedgehog came here from the future... a future where I didn't join the fight, and Eggman ruled the world. In that future the emerald is gone, the island is left in ruin, and I likely died trying to help after it was too late." He wearily sat down next to the emerald. "I don't have a choice this time Tikal."

The echidna girl glanced briefly at Chaos, who vanished back into the emerald a moment later. She watched him fade away, then moved to sit down next to Knuckles, folding her hands in her lap.

"I suppose you don't." She said softly. "I just hate to see conflict like this, Knuckles."

"If we don't fight, we lose everything," warned the guardian. "Eggman has already destroyed two cities, and either killed or captured Sonic. We need some way to fight back, or we don't have a chance in this war."

"You have the will to protect the emerald and the world." Tikal placed a reassuring hand on his shoulder. "And you have friends who will be there beside you."

"But will that be enough?" Knuckles shook his head. "We don't even know the extent of Eggman's power. If he can create something as strong as Perfect Chaos, then we need to get stronger as well."

"How?" Tikal questioned, her brow furrowing as she listened to the guardian's words.

Knuckles looked down at the glowing blue gemstone in his hand. "Gathering all the chaos emeralds is a long shot at this point. Shadow has one of them I'm sure, and if he's working for Eggman then who knows how many they might have? It won't be easy for us to get all of them. It might not even be enough to stop him if we did collect them all. But isn't there a way we could fight back using the Master Emerald instead?"

"What?" Tikal's eyes widened. "You can't just force the emerald to use its power for you."

"Why not?" Pressed Knuckles. "It's not like we would do anything bad with it's power, we'd only be using it to save the world from Eggman!"

"The world will still exist no matter what, Knuckles," she responded firmly, "You would be selfishly using the emerald's power to save _your_ idea of how the world should be."

"My idea?! You think Eggman's world is going to be better?"

"No, I don't. But you're missing the point."

"Explain it, then," he demanded.

"As Guardian, it is not for you to decide how and when the emerald should use its power. You may influence it, you may ask it to help you, but in the end you must remember that _you_ serve the _emerald_. It does not serve you. It _may_ decide to help you when you need it most, to preserve balance in the world. But it cannot be the answer to every problem."

Knuckles shook his head in defeat. "What other answer is there?"

She placed a comforting hand on his shoulder, her sky blue eyes staring into his violet ones. "That is something you and your friends must figure out together. Don't make the same mistake my father made. Don't try to force the Master Emerald to help you. The quickest path to power is saved for the greedy, and leads only to ruin. But the owner of a pure heart, who works hard to achieve strength, knows how to use that strength responsibly."

She reached for the chaos emerald he was still holding, cradling the glowing gem in her hands as she lifted it between them. "Don't underestimate the tools you already have in this fight. The true strength of these Chaos Emeralds lies in our hearts, not the Master Emerald. They transform our thoughts into power, and if your heart is pure, _anything_ is possible."

"Anything..." Knuckles repeated softly. "So we might not even need the Master Emerald's help?"

 _"If_ the time does come when there is truly no other answer, then the Master Emerald may act to help you. Just as it has done in the past." She glanced toward the glowing gem with a faint smile, as she continued her explanation: "When you first met Sonic, and Eggman stole the emerald, it acted of its own will to amplify the power of the Chaos Emeralds, giving Sonic enough power to defeat Eggman and rescue it. And when the Chaos Emeralds were powering the space colony ARK on its crash course to to the planet, the Master Emerald heeded your call and neutralized their power."

Turning back to face Knuckles, she spoke firmly and solemnly. "The Master Emerald _can_ help you, when all other hope is lost. But it does _not_ act on your terms. Trying to force your will upon it will only end in sorrow, as my father learned the hard way. If and when the time comes for the emerald to act, you will know it, Guardian. But until then, you must not make demands of it."

Tikal released her hold on the chaos emerald, and Knuckles let out a long sigh as he stared at the gem in his hand. "I understand." He said finally. "You have my word, I won't try to force the Master Emerald's power."

A gloved hand touched his chin, gently lifting his head up, and Tikal smiled at him comfortingly. "Go ahead with your search for the Chaos Emeralds. It may be a long and difficult task, but I _know_ you can succeed. Just remember what I said about where the true strength lies."

"In our hearts," the guardian recalled.

"And especially in a pure heart." Tikal grinned. "Never give up. You are strong, and your friends stand beside you. In the end, everything will turn out for the best."

Stepping back, the peach echidna folded her hands over her chest, giving Knuckles a final encouraging nod. Her body began to shimmer and slowly fade away, as her spirit was drawn back into the emerald. With a final murmur of "Good luck, Guardian." Tikal vanished completely, leaving Knuckles completely alone with his thoughts, deep within the silent halls of Hidden Palace.

* * *

That evening as the sun drew low on the western horizon, and shadows lengthened on the surface of Angel Island, Knuckles gathered the entire Resistance in the hollowed out cavern.

"I have some important news," he began, glancing around at each of his companions. Rouge, Silver, Tails, Amy, the Chaotix. Everybody was present. The guardian's gaze came to rest on the tired and battered telekinetic hedgehog, and he continued: "Silver, you fought well yesterday, but I'm afraid you didn't actually fight Chaos."

"What?" The hedgehog furrowed his brow. "What do you mean I didn't fight Chaos, what do you think I was doing?"

"I don't know what you fought," the echidna replied frankly, "but I know it wasn't Chaos, because that creature is still inside the Master Emerald. I saw it today with my own eyes."

"You've got _Chaos_ inside the emerald?" The white hedgehog exclaimed, eyes wide.

"He's been there the whole time, apparently," Knuckles commented matter-of-factly. "Completely harmless."

Tails put the pieces together quickly. "You managed to talk with Tikal, didn't you?"

"I did. She confirmed that whatever Silver fought yesterday, it wasn't the real Chaos."

"Wait a minute," Silver interrupted as he rubbed his forehead with his palm, "who on Mobius is Tikal?"

"Tikal is an ancestor of mine," began the echidna, "she sacrificed herself to stop Chaos' first rampage several thousand years ago, sealing herself and the beast in the Master Emerald."

Silver gaped for a moment, before shaking his weary head. "Never mind. But if I didn't fight Chaos yesterday, then what _did_ I fight? Whatever it was, it sure had the power of a water god."

"I don't know," the guardian replied with a frown, "but you're right. Whatever it was, it's incredibly powerful."

"How do we fight back against something that powerful, when we don't even know what it is?" Tails fretted.

Vector shrugged. "Silver seemed to hold his own against it yesterday."

The white hedgehog grimaced. "It wasn't exactly easy..."

"We must be ever on our guard," advised Espio, "vera few of us could last as long as Silver against such a powerful foe."

"Did Tikal give you any other tips, Knuckles?" Tails asked. "Any ideas on how we're supposed to win this?"

The echidna shook his head, recalling his ancestor's words of advice. "Only that searching for the Chaos Emeralds would be a good idea right now." He lifted his blue emerald for the while group to see. "But we only have one, and I don't even know where to begin looking for the others."

"I can help with that," replied the fox, his blue eyes lighting up with the spark of an idea as he reached for the glowing gem. "The Master Emerald acts as a unifier and controller for all the Chaos Emeralds. It might take a while, but I bet I could build a sensor to probe this emerald's connection with Master, and then use that data as a starting-point to find and follow the Master Emerald's connections to all the other Chaos emeralds!"

Knuckles handed the gem to the fox with a smile. "Smart idea, Tails. That will also give the rest of us time to recover and prepare for the next fight. Somehow I doubt we'll get to the Chaos Emeralds without a lot of trouble standing in the way."

"Speaking of preparing for the next fight, I have some news on that front." Rouge announced. "GUN lost a lot of drones and equipment in Metropolis yesterday, and the Commander doesn't want to risk a full scale fight like that again, unless it's absolutely necessary. That being said, Amy and I worked together and convinced him to approve shipments of weaponry and supplies for us here on the island, so that we can work together and continue helping everywhere we can."

"We may not be able to fight Eggman head-on," Amy explained, "but we can definitely be a thorn in his side, and help get the innocents out of danger."

"It's a good place to start," Knuckles decided. "we'll build ourselves up, hit Eggman anywhere we can, and work to find the Chaos Emeralds. And since we'll already be searching for those, there's no good reason why we shouldn't be searching for Sonic also."

Amy and Tails both instantly lit up at that news, as Knuckles continued to speak with a small grin on his face. "I have a feeling he's still out there, somewhere. If Sonic was really gone, Eggman wouldn't hesitate to rub it in our face - but he hasn't done that. If there's even the smallest chance Sonic is alive, we _have_ to try and save him." The guardian paused in reflection for a brief moment, before adding: "He would do the same for any of us."

The entire group raised their voices in agreement, and an instant later the red echidna almost lost his balance as Amy tackled him in a fierce hug. "Thank you, Knuckles."

"Yeah yeah, just save it for Sonic, ok?" He told the pink hedgehog with an embarrassed grin, extricating himself from her surprisingly strong embrace.

"I will," vowed Amy, with sharp determination etched on her youthful face. "I _know_ he's still alive, and I _know_ we'll find him."

The echidna shook his head at her typical unwavering faith, but pink hedgehog wasn't even paying attention to him. Her thoughts were with the one she loved, and she willed him to stay strong.

 _Wherever you are Sonic, just hang in there._ _I know you're out there somewhere, and I promise that I won't rest until you're back safe with us._

* * *

Meanwhile, in a secret facility far removed from Angel Island and the Resistance it harbored, a beaten and worn blue hedgehog was dragged harshly through a dim hallway. His wrists and ankles were tightly restrained by electric cuffs, and his face was set in a grimace. He had been held captive for nearly two weeks now, tortured and restrained, kept locked away from the rest of the world that needed his help. His face was filthy and haggard, and his body was covered in a patchwork of bruises, but Sonic the Hedgehog was most definitely still alive.

"So what are we doing today, Shadow?" He questioned the dark hedgehog who was currently dragging him by his ankles. "Another swimming lesson? Shock therapy? Or am I just your punching bag again today?"

The black and red hedgehog didn't deign to reply, simply continuing to drag his captive behind him through the dark corridor.

"You know, you could just let me out of these cuffs and we could have a race, for old time's sake." The hero continued with a rueful grin. "I won't even hold it against you that you're working for the Egghead."

Silence was again the only answer.

"Maria would probably hold it against you though."

A sharp backhand to the face was his reward for that remark, but Sonic wasn't phased. _That_ _never fails to get a reaction out of you, Shadow._ He smirked inwardly, taking what joy he could out of riling up his captor.

A moment later they reached the end of the corridor, and the hero was thrown roughly through an open door, landing in a heap at the feet of a widely grinning Eggman.

"Sonic, what a delight it is to see you again!"

"Wish I could say the same." Muttered the hedgehog, ignoring the bite of his restraints as he stood up.

"Ah, yes. Your confinement is getting to you, isn't it?" The mad genius cackled. "Maybe once I've finished conquering the world, I can find a bigger cell for you to sit in all day."

"Wow, doc. Your hospitality is really something."

Eggman ignored that remark, idly stroking his mustache as he began to speak. "I've brought you here to witness something, Sonic. Something that's been a long time in the making."

The hedgehog rolled his eyes. "Please, not another speech. Just get to torturing me, or whatever it is you're up to today."

The Doctor glanced quickly to Shadow, giving a brief nod, and the next instant a hover-skate slammed into his gut. "Insolent rodent!" The fat fiend sneered from above as Sonic doubled over in pain. "You'd do well to learn some respect for your new emperor."

In spite of the situation, and the pain in his stomach, the hero found himself laughing.

"Emperor?" He chuckled. "Really, Egghead?"

Another swift kick to his gut convinced him to stop laughing, as the evil genius stared down at him angrily.

"Yes, Sonic. Emperor. The time has finally come," Eggman spoke with a haunting grin. " _I've won._ You are my prisoner, and my glorious Eggman Empire is rising from the ashes of your world as we speak!"

The Doctor pressed a button at his wrist, and a holographic image materialized in front of the restrained hero. It was the city of Metropolis, once beautiful and proud in all it's urban glory - but what a terrible scene it now presented! Skyscrapers that had once gleamed splendidly were now battered and scarred, others had collapsed completely. Everywhere could be seen the scars of battle and tempest. Bridges were demolished, towers stood crumbling, and the roads were littered with wreckage and debris. Not a living being could be seen anywhere. Eggpawns alone roamed freely through the rubble-strewn streets, already beginning the work of transforming the sprawling city into a massive robotic stronghold.

As Sonic watched in guilt and horror, the scene changed to a view of the tallest tower in the city, a spiraling structure that had once been home to the government of Metropolis. Now, on the spire at the very top of that magnificent structure, a black flag was hoisted and unfurled, bearing the fearsome insignia of the Eggman Empire.

"Your friends tried to fight," taunted the Doctor, "but they were no match for my forces. Robotropolis will make a fine capital for my new Empire."

"Robotropolis? Your new..." Sonic shook his head, baring his teeth in anger. The rage and frustration he felt right now was overwhelming. "What did you do to my friends?!"

"Wouldn't you like to know."

"Robotnik!" He fumed as he struggled against his restraints, reverting to the scientist's true name in his rage. "If you hurt them..."

"Robotnik?" Repeated the Doctor in confusion. "After all these years, are you finally taking me seriously enough to use my real name?"

"Answer my question!"

"No," Eggman replied with a devious smirk, "I don't think I will."

He growled, lunging awkwardly at the villain despite his restraints. Shadow intervened in an instant, forcefully kicking the hero across the room, where he impacted the wall with a thud. All Sonic could see at this point was red. He was furious at Eggman, and at Shadow. He was frustrated that he couldn't do anything to stop this. He was terrified for his friends. He felt guilty that he had failed. All that anger and frustration and guilt - all that negative emotion inside him - was to much to hold back. For the briefest of instants, his blue fur darkened, and his eyes flashed pure white. Then it was over, and he collapsed in a dead faint on the cold metal floor below.

* * *

 _Poor Sonic isn't having a very good time. :(_

 _ **Author's Note:**_

 _Wew. This was a tough chapter to write_ _. Some deep and serious things going on in this one. Not really any fighting action, but a lot of important character scenes. I hope Tikal's explanations didn't get too confusing. I wanted to show some of Knuckles desperation to find a solution here, and I also wanted her to explain things as well as possible, because it sets up some important themes later in the story._

 _Anyways, I hope you all enjoyed this chapter. I'm happy to answer any questions you have, and I appreciate all suggestions or opinions on the story. The next chapter will hopefully not take as long as this one, I'm impatient to keep the story moving forward quickly. :)_

 _(Question of the day: What do you folks think of the new Sonic racing game?)_


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